Detection of human papillomavirus by the polymerase chain reaction

ABSTRACT

The presence of human papillomavirus (HPV) in a sample can be detected and the HPV typed by a method that involves the amplification of HPV DNA sequences by the polymerase chain reaction (PCR). The primers used in the method are consensus primers that can be used to amplify a particular region of the genome of any HPV. The presence of HPV in a sample is indicated by the formation of amplified DNA. The HPV nucleic acid is detected by consensus probes that may be short oligonucleotide probes or long generic probes. The HPV is typed by the use of type-specific DNA probes specific for the amplified region of DNA.

This application is a continuation of application Ser. No. 08/126,452, filed Sep. 24, 1993, now abandoned, which is a continuation-in-part of U.S. Ser. No. 08/050,743, filed Apr. 20, 1993, now U.S. Pat. No. 5,447,839, which is a continuation of U.S. Ser. No. 07/613,142, filed Nov. 14, 1990, now abandoned, which is a continuation-in-part of PCT/US89/03747, filed Sep. 9, 1989, which is a continuation-in-part of U.S. Ser. No. 322,550, filed Mar. 10, 1989, which issued as U.S. Pat. No. 5,182,377, which is a continuation-in-part of U.S. Ser. No. 243,486, filed Sep. 9, 1988, now abandoned, each of which is incorporated herein by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention provides medical research and diagnostic methods and reagents for detecting and typing HPV.

The methods utilize PCR, a DNA amplification technique widely used in the fields of molecular biology and genetic engineering. The methods can also be used to generate information concerning previously unknown types and sub-types of HPV and consequently has applications in the field of virology.

2. Description of Related Art

Papillomaviruses have been linked to widespread, serious human diseases, especially carcinomas of the genital and oral mucosa. And although genital HPV infection is associated with cancer primarily in women, recent evidence suggests that HPV may play a role in the development of anogenital cancers in men. Broker et al., 1986, Cancer Cells 4:17-36, review the molecular, cellular, and clinical aspects of the papillomaviruses and the relationship of HPVs to cancer. HPV types 6, 11, 16, 18, and 33 are known genital HPV types in the human population, and Broker et al., 1986, Cancer Cells 4:589-594, disclose that HPV types 6, 11, 16, 18, and 33 share significant homology at the DNA level, particularly at the L 1 open reading frame.

Identification and typing of HPV is quite important, because different types of HPV pose different risks to the affected individuals. For instance, HPV16 and HPV18 have been more consistently identified in higher grades of cervical dysplasia and carcinoma than other HPV types. Webb et al., December 1987, J. Inf. Disease 156(6):9 12-919, report a method for detecting HPV DNA types that utilizes a reverse-blotting procedure. The procedure involved forming a membrane to which genomic DNA from four different HPV types was bound and then hybridizing labeled DNA from a biological sample to the DNA bound to the membrane. Caussey et al., February 1988, J. Clin. Microbiol. 26(2):236-243 describe similar HPV detection methods.

Shibata et al., January 1988, J. Exp. Med. 167:225-230, disclose the use of PCR to amplify and detect the presence of HPV 16 and HPV 18 DNA. U.S. Pat. Nos. 4,683,195 and 4,683,202 disclose PCR and the use of PCR to detect the presence or absence of nucleic acid sequence in a sample. PCT Pat. Publication No. WO 90/02821 discloses the use of consensus primers and probes to amplify and detect HPV sequences in a sample. The publication also describes type-specific probes for typing the HPV DNA if present in the sample.

Maitland et al., May 1988, Seventh International Papillomavirus Workshop, Abstract, p. 5, report the use of PCR to detect HPV 16 in oral and cervical biopsies. In addition, Campione-Piccardo et al., May 1988, Seventh International Papillomavirus Workshop, Abstract, p. 19, report the use of a mixture of primers for the specific amplification by PCR of HPV sequences in types 1a, 5, 6a, 6b, 8, 11, 16, 18, and 33. A number of other researchers disclosed the use of PCR to amplify and detect HPV sequences at the Seventh International Papillomavirus Workshop. Each of the background references described in this section is incorporated herein by reference.

The heterogeneity of the human papillomavirus group is generally described in deVilliers, 1989, J. Virology 63:4898-4903, which is incorporated herein by reference. The genomes of numerous HPV types have been sequenced and/or characterized. For example, for HPV type 6, see deVilliers et al., 1981, J. Virology 40:93214 935, and Gissmann and Zur Hausen, 1980, Int. J. Cancer 25:605-609, and Schwartz et al., 1983, EMBO J. 2(12):2341-2348. For HPV type 2, see Gissmann et al, 1982, J. Virology 44:393-400. For HPV type 11, see Dartmann et al., 1986, Virology 151:124-130. For HPV type 16, see Seedorf et al, 1985, Virology 145:181-185. For HPV type 18, see Cole and Danos, 1987, J. Mol. Biol. 93:599-608. For HPV type 31, see Goldsborough et al., 1989, Virology 171:306-311. For HPV 33, see Cole and Streeck, 1986, J. Virology 58:991-995. For HPV 54, see Favre et al., 1990, Int. J. Cancer 45:40-46. For HPV 56, see Lorincz, 1989, J. Gen. Virol. 70:3099. These publications are incorporated herein by reference.

Despite the use of PCR to amplify and detect HPV sequences, there still remains a need for a simple and rapid method for both detecting and typing HPV in a biological sample. Pat. Publication No. PCT/US89/03747 describes improved methods that offer speed and simplicity for detection and typing HPV in a sample. The methods comprise amplifying a sequence of HPV DNA present in the sample, determining if amplification has occurred and then hybridizing an HPV type-specific probe to the amplified DNA.

SUMMARY OF THE INVENTION

The present invention provides novel compositions and methods for amplifying and typing HPV nucleic acids.

One aspect of the invention relates to novel HPV sequences.

Another aspect of the invention relates to sequence specific probes for determining the HPV type or isolate present in a sample. These novel sequence specific probes enable the detection of previously unknown HPV types and subtypes.

Another aspect of the invention relates to novel primers for amplifying HPV sequences using the polymerase chain reaction. Novel primers are provided for improved amplification of HPV-51. An improved primer pair is provided for the generic amplification of the L1 region of HPV nucleic acids.

Another aspect of the invention relates to methods for classifying an HPV contained in a sample, wherein the methods comprise the steps of:

(a) amplifying HPV nucleic acid;

(b) treating portions of the amplified product formed in step (a) under hybridizing conditions with sets of probes, wherein each set of probes enables the specific detection of a class of HPV types; and

(c) determining the classification of the HPV by the occurrence of hybridization with a probe set.

Another aspect of the invention relates to methods for typing an HPV contained in a sample, wherein the methods comprise the steps of:

(a) amplifying HPV nucleic acid using the polymerase chain reaction (PCR) using a set of primer pairs which enables the amplification of nucleotide sequences of HPV types 6, 11, 16, 18, and 33;

(b) wearing the amplified product formed in step (a) under hybridizing conditions with a sequence specific probe which enables the specific detection of an HPV type selected from the group of HPV types consisting of HPV types 26, 31, 35, 39, 40, 42, 45, 51, 52, 53, 54, 55, 56, 57, and 59; and

(c) determining the HPV type by the occurrence of hybridization with the probe.

DETAILED DESCRIPTION OF THE INVENTION

To aid in understanding the invention, several terms are defined below.

The terms "nucleic acid" and "oligonucleotide" refer to primers, probes, and oligomer fragments to be detected, and shall be generic to polydeoxyribonucleotides (containing 2-deoxy-D-ribose), to polyribonucleotides (containing D-ribose), and to any other type of polynucleotide which is an N glycoside of a purine or pyrimidine base, or modified purine or pyrimidine base. There is no intended distinction in length between the terms "nucleic acid" and "oligonucleotide", and these terms will be used interchangeably. These terms refer only to the primary structure of the molecule. Thus, these terms include double- and single-stranded DNA, was well as double- and single-stranded RNA.

The exact size of an oligonucleotide depends on many factors and the ultimate function or use of the oligonucleotide. Oligonucleotides can be prepared by any suitable method, including, for example, cloning and restriction of appropriate sequences and direct chemical synthesis by a method such as the phosphotriester method of Narang et al., 1979, Meth. Enzymol. 68:90-99; the phosphodiester method of Brown et al., 1979, Meth. Enzymol. 68:109-151; the diethylphosphoramidite method of Beaucage et al., 1981, Tetrahedron Lett. 22:1859-1862; and the solid support method of U.S. Pat. No. 4,458,066, each incorporated herein by reference. A review of synthesis methods is provided in Goodchild, 1990, Bioconjugate Chemistry 1(3):165-187, incorporated herein by reference.

The term "target region" refers to a region of a nucleic acid which is to be analyzed.

The term "hybridization" refers the formation of a duplex structure by two single stranded nucleic acids due to complementary base pairing. Hybridization can occur between complementary nucleic acid strands or between nucleic acid strands that contain minor regions of mismatch. Conditions under which only complementary nucleic acid strands will hybridize are referred to as "stringent hybridization conditions." Two single-stranded nucleic acids that are complementary except for minor regions of mismatch are referred to as "substantially complementary". Stable duplexes of substantially complementary sequences can be achieved under less stringent hybridization conditions. Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length and base pair concentration of the oligonucleotides, ionic strength, temperature, and incidence of mismatched base pairs.

The term "probe" refers to an oligonucleotide which forms a duplex structure with a sequence of a target nucleic acid due to complementary base pairing. The probe will contain a "hybridizing region", which is a region of the oligonucleotide corresponding to a region of the target sequence. "Corresponding" means identical to or complementary to the designated nucleic acid. A probe oligonucleotide can either consist entirely of the hybridizing region or can contain additional features which allow for the detection or immobilization of the probe but do not alter the hybridization characteristics of the hybridizing region.

As used herein, the term "probe" also refers to a set of oligonucleotides, wherein the oligonucleotides of the set provide sufficient sequence variants of the hybridization region to enable hybridization with each member of a given set of target sequence variants. For example, because within each HPV type are found subtypes which contain minor sequence variants, a type-specific probe may contain a set of oligonucleotides for hybridization with each of the subtype variant sequences. Additionally, a probe may consist of one or more oligonucleotides which contain mismatches with some or all members of a given set of target sequence variants, but contains sufficient regions of complementarity with each target sequence variant so as to enable hybridization with all target sequence variants under suitable conditions. The term "consensus probes" is used herein to refer to single oligonucleotides complementary to a consensus target sequence, to probes consisting of multiple oligonucleotides, and to combinations thereof.

The terms "sequence-specific oligonucleotide" and "SSO" refer to oligonucleotide probes wherein the hybridization region is exactly complementary to the sequence to be detected. The use of stringent hybridization conditions under which the probe will hybridize only to that exactly complementary target sequence allows the detection of the specific target sequence. Stringent hybridization conditions are well known in the art (see, e.g., Sambrook et al., 1985, Molecular Cloning--A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. incorporated heroin by reference). Stringent conditions are sequence dependent and will be different in different circumstances. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the base pairs have dissociated. Typically, stringent conditions will be those in which the salt concentration is at least about 0.2 molar at pH 7 and the temperature is at least about 60° C. Relaxing the stringency of the hybridizing conditions will allow sequence mismatches to be tolerated; the degree of mismatch tolerated can be controlled by suitable adjustment of the hybridization conditions.

The term "primer" refers to an oligonucleotide, whether natural or synthetic, capable of acting as a point of initiation of DNA synthesis under conditions in which synthesis of a primer extension product complementary to a nucleic acid strand is induced, i.e., in the presence of four different nucleoside triphosphates and an agent for polymerization (i.e., DNA polymerase or reverse transcriptase) in an appropriate buffer and at a suitable temperature. A primer is preferably a single-stranded oligodeoxyribonucleotide. The appropriate length of a primer depends on the intended use of the primer but typically ranges from 15 to 35 nucleotides. Short primer molecules generally require cooler temperatures to form sufficiently stable hybrid complexes with the template. A primer need not reflect the exact sequence of the template but must be sufficiently complementary to hybridize with a template. Primers can incorporate additional features which allow for the detection or immobilization of the primer but do not alter the basic property of the primer, that of acting as a point of initiation of DNA synthesis.

As used herein, the term "primer" also refers to a set of oligonucleotides, wherein the oligonucleotides of the set provide sufficient sequence variants of the hybridization region to enable hybridization with each member of a given set of target sequence variants, so as to act as a point of initiation of DNA synthesis. Additionally, a primer may consist of one or more oligonucleotides which contain mismatches with some or all members of a given set of target sequence variants, but contains sufficient regions of complementarity with each target sequence variant so as to enable hybridization with all target sequence variants under suitable conditions. The term "consensus primers" is used herein to refer to single oligonucleotides complementary to a consensus target sequence, to primers consisting of multiple oligonucleotides, and to combinations thereof.

The term "thermostable polymerase enzyme" refers to an enzyme that is relatively stable to heat and catalyzes the polymerization of nucleoside triphosphates to form primer extension products that are complementary to one of the nucleic acid strands of the target sequence. The enzyme initiates synthesis at the 3' end of the primer and proceeds in the direction toward the 5' end of the template until synthesis terminates. A purified thermostable polymerase enzyme is described more fully in U.S. Pat. No. 4,889,818, incorporated herein by reference, and is commercially available from Perkin-Elmer, Norwalk, Conn.

Amplification of DNA by the polymerase chain reaction (PCR) is disclosed in U.S. Pat. Nos. 4,683,195, 4,683,202, and 4,965,188, which are incorporated herein by reference. PCR amplification of DNA involves repeated cycles of heat-denaturing the DNA, annealing two oligonucleotide primers to sequences that flank the DNA segment to be amplified, and extending the annealed primers with DNA polymerase. The primers hybridize to opposite strands of the target sequence and are oriented so DNA synthesis by the polymerase proceeds across the region between the primers, effectively doubling the amount of that DNA segment. Moreover, because the extension products are also complementary to and capable of binding primers, each successive cycle essentially doubles the amount of DNA synthesized in the previous cycle. This results in the exponential accumulation of the specific target fragment, at a rate of approximately 2^(n), where n is the number of cycles.

Due to the enormous amplification possible with the PCR process, small levels of DNA carryover from samples with high DNA levels, positive control templates or from previous amplifications can result in PCR product, even in the absence of purposefully added template DNA. If possible, all reaction mixes are set up in an area separate from PCR product analysis and sample preparation. The use of dedicated or disposable vessels, solutions, pipettes (preferably positive displacement pipettes), and pipette tips (preferably with aerosol barriers) for RNA/DNA preparation, reaction mixing, and sample analysis will minimize cross contamination. See also Higuchi and Kwok, 1989, Nature 339:237-238 and Kwok, and Orrego, in Innis et al. eds., 1990 PCR Protocols: A Guide to Methods and Applications, Academic Press, Inc., San Diego, Calif., which are incorporated herein by reference.

Methods to reduce the problem of contamination of a PCR by the amplified nucleic acid from previous reactions are described in PCT patent publication U.S. Ser. No. 91/05210 and U.S. Pat. No. 5,035,996, both incorporated herein by reference. The methods allow the enzymatic degradation of any amplified DNA from previous reactions. PCR amplifications are carried out in the presence of dUTP instead of dTTP. The resulting double-stranded amplification product which incorporates uracil is subject to degradation by uracil-N-glycosylase (UNG), whereas normal thymine-containing DNA is not degraded by UNG. Amplification reaction mixtures are treated with UNG before amplification to degrade all uracil-containing DNA that could serve as target. Because the only source of uracil-containing DNA is the amplified product of a previous reaction, this method effectively eliminates the problem of contamination from previous reactions (carryover). UNG is rendered temporarily inactive by heat, so the denaturation steps in the amplification procedure also serve to inactivate the UNG. New amplification products, therefore, though incorporating uracil, are formed in an UNG-inactivated environment and are not degraded.

Although the polymerase chain reaction is the preferred amplification method, amplification of target sequences in a sample may be accomplished by any known method, such as ligase chain reaction (Wu and Wallace 1988, Genomics 4:560-569, incorporated herein by reference), the TAS amplification system (Kwoh et al., 1989, Proc. Natl. Acad. Sci. USA 86:1173-1177, incorporated herein by reference), and self-sustained sequence replication (Guatelli et al., 1990, Proc. Natl. Acad. Sci. USA 87:1874-1878, incorporated herein by reference), each of which provides sufficient amplification so that the target sequence can be detected by nucleic acid hybridization to an SSO probe. Alternatively, methods that amplify the probe to detectable levels can be used, such as Qβ-replicase amplification (Kramer and Lizardi, 1989, Nature 339:401-402, and Lomeli et al., 1989, Clin. Chem. 35:1826-1831, both of which are incorporated herein by reference). A review of known amplification methods is provided in Abramson and Myers, 1993, Current Opinion in Biotechnology 4:41-47, incorporated herein by reference. The term "probe", as used herein, encompasses the sequence-specific oligonucleotides used in the above procedures; for instance, the two or more oligonucleotides used in LCR are "probes" for purposes of the present invention, even though some embodiments of LCR only require ligation of the probes to indicate the presence of an allele.

The choice of primers for use in PCR determines the specificity of the amplification reaction. In the amplification steps of the method of the present invention, "consensus" primers are used that will amplify HPV sequences present in a sample, regardless of type. The consensus primers of the invention can include degenerate primers, mixtures of the oligonucleotides synthesized so that any one of several nucleotides can be incorporated into a primer at a selected position during synthesis. The consensus primers are sufficiently complementary to all types of HPVs to amplify a DNA sequence of any HPV present in the sample. The consensus primers are also designed to amplify a region of DNA that contains sequences that are specific to each major viral type, so the amplified DNA can therefore be used to type the HPV present in the sample. The consensus primers may also be suitable in a ligase chain reaction. For example, in PCT Pat. Publication No. WO 89/09835, a process is described that involves the use of ligase to join oligonucleotide segments that anneal to the target nucleic acid. This publication is incorporated herein by reference.

Primers of the invention are generally 18 to 21 nucleotides in length and are designed to have a high degree of homology with HPV sequences. For instance, in the design of the genital HPV consensus primers of the invention, a high degree of homology with all five major genital HPVs (HPV types 6, 11, 16, 18, and 33) was required. The consensus primers also are highly homologous to HPV31 (Goldsborough et al., 1989, Virology 17l:306-311). For each region to be amplified, two regions of homology are required, one for negative-strand primers and another for positive-strand primers. To identify a homologous region, viral sequences are compared. Once a homologous region is identified, a consensus primer is designed. Degenerate bases can be used in the design to accommodate positions at which an individual virus varies in sequence from the consensus sequence. Preferably, as many degenerate positions are made as is necessary so that all viral sequences have fewer than three mismatches with the consensus primer. The degenerate positions are chosen so that the smallest number of degenerate bases accommodates the largest possible number of viral sequences.

If a particular viral sequence has a large number of mismatches with the consensus sequence, then a type-specific primer is made for that virus. The type-specific primer is mixed with the degenerate primer that was designed for other viruses to make the consensus primer. Any mismatches that are not accommodated by the degenerate positions in the primer should generally be located more than 3 bases from the 3' end of the primer. Likewise, any degenerate positions should be more than 3 bases from the 3' end of the primer.

Estimated minimum and maximum T_(m) s for a degenerate primer should be between 54° C. and 64° C. T_(m) s are estimated by the non-empirical formula: each G or C contributes 4 degrees C. to the T_(m) ; each A or T contributes 2° C. to the T_(m) ; and the T_(m) is the sum of the calculated values. Finally, primers should not be designed to span palindromes or repetitive sequences.

The consensus primers of the present invention can also be used to detect HPV types previously uncharacterized. For instance, HPV isolate 88 noted in Table 4 has previously not been reported. Thus, the consensus primers of the invention can be used to amplify DNA sequences of previously unknown HPV types. The amplified DNA can then be sequenced and the sequence data used to generate type-specific probes for use in the method of the present invention.

The present methods have led, and will continue to lead, to the discovery of many previously unknown or uncharacterized HPV types. However, with each new HPV type discovered there comes a corresponding need to make the consensus probe more generic to ensure that the new type will be detected and to make type-specific probes. These new HPV types, primers for amplifying the new types, and probes for detecting and distinguishing the new types are an additional aspect of the present invention.

The first step of the preferred method involves the amplification of an HPV sequence, if that sequence is present in a sample, by PCR using consensus primers. Illustrative consensus primers of the invention are referred to by the region of the HPV genome the primers are used to amplify. The HPV genome is circular. The genome of genital HPVs is oriented as follows: E6, E7, E1, E2, E4, E5a, E5b, L2, L1, and URR. "E" and "L" designations indicate open reading frames and URR indicates the transcriptional regulatory region. Several of the open reading frames overlap, for example, the E4 region is totally contained within the E2 open reading frame. Primers can be used to amplify a sequence that spans one or more regions of the HPV genome. The methods and compositions described herein are particularly suited for amplifying the following HPV regions: L1/URR, L1, E6, E6/E7, E7 through E1, E6 through E1, and E 1. It will be clear to one of ordinary skill in the art that the methods disclosed are applicable to any region of the HPV genome and are not limited to the specific embodiments described herein.

Following amplification, a determination is made as to whether amplification has occurred. There are a variety of known means for determining whether amplification has occurred. For example, a portion of the PCR reaction mixture can be subjected to gel electrophoresis and the resulting gel stained with ethidium bromide and exposed to ultraviolet light to observe whether a product of the expected size is present. Alternatively, labeled PCR primers or deoxyribonucleoside 5'-triphosphates are utilized and incorporation of the label into the amplified DNA is determined by, for example, gel electrophoresis and autoradiograph to ascertain if amplification occurred.

Another method for determining if amplification has occurred is to test a portion of PCR reaction mixture for ability to hybridize to a labeled probe designed to hybridize to only the amplified DNA. Probes which hybridize to all HPV types are useful for detecting if amplification has occurred. The present invention provides both consensus and generic probes for the non-type-specific detection of HPV. Alternatively, the determination of amplification and identification of HPV type can be carried out in one step by testing a portion of the PCR reaction mixture for its ability to hybridize to one or more type-specific probes.

Long generic probes provide an alternative to short consensus oligonucleotide probes. Long generic probes comprise all or most of the HPV genomic sequence that lies between the HPV amplification primers. The sequences of one or more HPV types may be combined to provide long probes for enhanced sensitivity and to reduce the likelihood of a false negative result even when a novel variant HPV-type is present. The length of long generic probes increases the hybridization stability and, hence, the tolerance for mismatches.

As used herein, the terms "long probes," "generic probes," and "long generic probes" all refer to nucleic acid segments used as generic probes for determining if amplification of any HPV has occurred. Long probes are generally greater than 100 nucleotides in length and may be as long as the amplified fragment they are designed to detect. Preferably, long probes are between 100-600 base pairs in length and comprise the full length of the amplified fragment to be detected, but do not include the primer sequences used to generate the amplified segment. For example, in Example 2, the long probes are 410 nucleotides long (450, the L1 amplified product length--2×20, the L1 consensus primer length). The long probes are preferably PCR fragments. Most preferably, the PCR primers used to prepare the long probes are nested primers relative to the consensus primers used to amplify the HPV DNA in a sample so that the consensus primer sequences are not included in the probe.

The long probes of the invention may be used in a mixture suitable for generic detection of HPV nucleic acids. However, it is not necessary to include amplified nucleic acids from each major HPV type in a long generic probe mixture in order to achieve generic detection of HPV nucleic acids. In one embodiment, described in Example I, long probes are prepared using HPV-16, HPV-18, and two clinical samples as the PCR template. The example describes a mixture of 410 base pair probes that hybridize to the major HPV types, as well as minor, variant, or novel HPV types. An alternate long probe with modified type specificity is described in Example 4. The long probes may be single-stranded or double-stranded.

Short oligonucleotide consensus probes design is similar to consensus primer design, except that consensus probes generally do not contain as many mismatches as consensus primers. As a result, the T_(m) for a probe can be higher than the T_(m) for a primer. However, where a mismatch or degenerate position occurs with respect to the 3' end is not as critical for consensus probes as it is for consensus primers. Clearly, long probes can tolerate a greater number of mismatches.

Type-specific probes are designed so that a given probe will generally have less than 75% similarity with sequences from HPV types distinct from that recognized by the probe. The type-specific probes are usually 18-20 nucleotides in length with estimated T_(m) s in the range of 58° C. to 64° C. The present invention also describes that more than one type-specific probes may be employed for typing. This aspect of the invention provides additional assurance that variant types will be correctly detected and typed. Preferably two type-specific probes are employed that are capable of hybridizing to opposite strands and residing in separate regions of the amplified product.

Thus, an important aspect of the present invention relates to the novel probes provided for use in the present methods. Whether these probes are consensus or generic probes for determining if amplification has occurred or type-specific probes, the probes can be used in a variety of different hybridization formats. Although solution hybridization of a nucleic acid probe to a complementary target sequence is clearly within the scope of the present invention, commercialization of the invention will likely result in the use of immobilized probes and thus a quasi "solid-phase" hybridization.

In one format, referred to as a "dot blot" assay or "forward dot blot" assay, the amplified target is immobilized on a solid support and the target sequences are then hybridized to the labeled probe. The unhybridized fraction of the probe is then removed by washing under suitably stringent conditions, and the support is monitored for the presence of hybridization duplexes.

An alternate method that is quite useful when large numbers of different probes are to be used is a "reverse" dot blot format, in which the amplified sequence is labeled and the probes are immobilized. In this format, unlabeled sequence-specific probes are bound to a membrane and exposed to the labeled sample under appropriately stringent hybridization conditions. Unhybridized labeled sample is then removed by washing under suitably stringent conditions, and the membrane is then monitored for the presence of hybridization duplexes. In one method, the probes are attached to a solid support by virtue of long stretches of T residues; these T residues are added to the probe during synthesis of the probe on an automated synthesizer after the hybridizing sequence is synthesized. When long probes are used in the method, T-tailing is unnecessary, and the probes can be attached directly to the solid support.

Both the forward and reverse dot blot assays can be carried out conveniently in a microwell plate; see U.S. Ser. No. 695,072, filed May 3, 1991, which is a CIP of U.S. Ser. No. 414,542, filed Sep. 29, 1989, now abandoned, incorporated herein by reference. The probes can be attached to bovine serum albumen (BSA), for example, which adheres to the microwell plate, thereby immobilizing the probe.

For classifying HPV types into groups of types, such as oncogenic and non-oncogenic types, as described in Example 7, it is not necessary to distinguish among the types within each group. It is sufficient to detect hybridization with any of a number of type-specific probes. In this case, it is desirable to pool probes. However, the total number of probes which can be attached to a microwell plate by either passive coating or by adsorption of probes conjugated to bovine serum albumin (BSA) is limited. Because the total number of bound probes is constant, pooling probes can decrease the number of each probe and, hence, decrease sensitivity. On method of maintaining sensitivity is to incorporate multiple hybridizing sequences in each probe. Probe hybridizing sequences can be linked such that a multiplicity of hybridizing sequences are attached to the plates through a single binding site. In a preferred method, each probe contains between two and four probe hybridizing sequences linked linearly. A linked probe structure can be a single oligonucleotide containing a series of individual probe sequences arranged consecutively. Alternatively, individual probe oligonucleotides sequences may also be attached to each other through spacers of various lengths. Probes may also be constructed using a branching structure such that the hybridizing regions are each attached to the same base structure, or in structures that are hybrids of a linear and branched structure.

Another suitable assay system is described in U.S. Ser. No. 563,758, filed Aug. 6, 1990, incorporated herein by reference, in which a labeled probe is added during the PCR amplification process. Any SSO probe that hybridizes to target DNA during each synthesis step is degraded by the 5' to 3''exonuclease activity of a polymerase, e.g., Taq polymerase. The degradation product from the probe is then detected. Thus, the presence of the breakdown product indicates that the hybridization between the SSO probe and the target DNA occurred.

Many methods for labeling nucleic acids, whether probe or target, are known in the art and are suitable for purposes of the present invention. Suitable labels may provide signals detectable by fluorescence, radioactivity, colorimetry, X-ray diffraction or absorption, magnetism, enzymatic activity, and the like. Suitable labels include fluorophores, chromophores, radioactive isotopes (particularly ³² P and ¹²⁵ I), electrondense reagents, enzymes and ligands having specific binding partners. Enzymes are typically detected by their activity. For example, horse-radish-peroxidase (HRP) can be detected by its ability to convert diaminobenzidine to a blue pigment. A preferred method for HRP based detection uses tetramethyl-benzidine (TMB) as described in Clin. Chem. 33: 1368 (1987). An alternative detection system is the Enhanced Chemiluminescent (ECL) detection kit commercially available from Amersham, Arlington Heights, Ill. The kit is used in accordance with the manufacturer's directions.

Probes may be labeled with radioactive phosphorous ³² P, by treating the probes with polynucleotide kinase in the presence of radiolabeled ATP. However, for commercial purposes non-radioactive labeling systems may be preferred, such as, horseradish peroxidase-avidin-biotin or alkaline phosphatase detection systems. HRP can be used in a number of ways. For example, if the primer or one or more of the dNTPs utilized in a PCR amplification has been labeled (for instance, the biotinylated dUTP derivatives described by Lo et al., 1988, Nuc. Acids Res. 16:87 19) instead of the probe, then hybridization can be detected by assay for the presence of labeled PCR product. In a preferred embodiment, probes are biotinylated and detected with the ECL system described above. For example, biotinylated probes were prepared by direct biotinylation of the oligonucleotide rather than incorporation of biotin-dUTP during PCR. For 5' biotinylation of oligonucleotides direct solid phrase synthesis using biotin containing phosphoramidites was done according to Alves et al., 1989, Tetra. Let 30:3098; Cocuzza, 1989, Tetra Let. 30:6287; and Barabino et al., 1989, EMBO J. 8:4171. Solid phase synthesis of biotinylated oligonucleotides at any internal or terminal (5' or 3') position is also suitable for preparing biotinylated primers and probes (Pieles et al., 1989, NAR 18:4355, and Misiura et al., 1989, NAR 18:4345).

Alternatively, biotinylated probes can be prepared using terminal deoxynucleotide transferase (TdT) (Boeringer Mannheim) as follows. An 8:1 molar ratio of biotin-dUTP: oligonucleotide provided 80% derivatization with each molecule bearing 1 or more terminal biotin dUMPs. The tailing reaction contained 100 pmoles of oligonucleotide and 800 pmoles of biotin-dUTP in a 10-20 μl reaction using 3-10 units of TdT for 30-60 minutes at 37° C. The reaction buffer was prepared according to the enzyme specifications from the manufacturer. The reaction was stopped with EDTA and purified from 2.5M NH₄ Ac, by ethanol precipitation (twice) using 10 μg tRNA, ssDNA, glycogen or linearized acrylamide as a carrier (see Focus 11(3):57-58). Tailed oligonucleotides can be probes for targets fixed to a solid support. The Amersham ECL system provides an appropriate means for detecting these compounds (see Nature 346:297 [1990]).

In one embodiment of the invention biotinylated probes are prepared by incorporating biotin-dUTP into the amplification reaction for preparing long probes.

Alternatively, probes are conjugated to HRP, for example, according to the method disclosed in WO 89/2932, and Beaucage et al., 1981, Tetra. Lett. 22:1859-1862. These references are incorporated herein by reference. For HRP conjugated probes, the hybridization buffer is adjusted to decrease the wash temperature required for removing non-specifically hybridized probe without the risk of denaturing the HRP enzyme. However, HRP conjugated probes are not used in the preferred embodiment. Whatever the labeling system used, once a determination has been made that the L1 consensus probe has hybridized to amplified DNA present in the sample, the amplified DNA is typed to determine the HPV types present in the sample.

Those skilled in the art also recognize from the present disclosure that the method of the present invention can be carried out in a variety of ways. The present method is applicable to any human papillomavirus and especially preferred for detecting and typing genital HPVs. The method can be used to detect isolate-to-isolate variation within a particular HPV type and can also be used to screen for significant changes in the HPVs present in a patient. In one embodiment of the invention, consensus primers to more than one region of HPV DNA will be used, ensuring that if any portion of the HPV genome has been deleted, other regions can still be detected. In a similar fashion, the typing of the amplified DNA can be done using a variety of type-specific probes that recognize different regions of the amplified DNA. In a preferred embodiment, probes capable of hybridizing to at least two regions of the amplified DNA are employed to increase the likelihood of correctly typing HPV variants.

An internal amplification control is preferably used to assure the competency of a sample for amplification and reduce the likelihood of false negative results. The internal control can be a genomic segment of DNA known to be present in a sample of human origin. For example, the β-globin gene provides a suitable positive control amplification target. In one embodiment of the invention, β-globin primers are included in the PCR reaction mixture for amplifying the L1 region of the HPV genome. β-globin primers GH20 (Seq ID No. 101) and PC04 (Seq ID No. 102) produce a 268 base pair product.

    ______________________________________                                         GH20   Seq ID No. 101                                                                             GAAGAGCCAAGGACAGGTAC                                        PC04   Seq ID No. 102                                                                             CAACTTCATCCACGTTCACC                                        ______________________________________                                    

The β-globin amplified segment is readily distinguished from the L 1 amplified product using gel electrophoresis by size (268 bp vs. 450 bp). For a positive control, when E6 consensus primers are used, other methods of detecting the β-globin product are desirable because the E6 product is 240 base pair in size and, therefore, is not necessarily easily distinguished. In that event, a β-globin probe can be used to detect the amplified product; PC03 (Seq ID No. 103) is a suitable oligonucleotide probe.

    ______________________________________                                         PC03   Seq ID No. 103                                                                             ACACAACTGTGTTCACTAGC                                        ______________________________________                                    

Alternatively, the β-globin and HPV amplification reactions can be run in parallel and analyzed individually. Similarly, it may be desirable to include positive and negative HPV controls in practicing the present methods for detecting and typing any HPV. For example, in one embodiment of the invention, plasmids containing genomic segments of HPVs 6, 11, 16, 18, and 33 are included. So long as the consensus primers, probes and type-specific probes used in the method can amplify and hybridize to the control nucleic acid, it is not essential that the control comprises the entire viral genome of each HPV. Example 2 describes specific HPV plasmids used as positive control; however, these specific plasmids are non-essential aspects of the invention and numerous cloned HPVs are described in the literature.

Those skilled in the art recognize that the present invention can also be used to detect HPV mRNA present in a sample. The expression of certain HPV mRNA species, particularly E6 and E7 mRNAs, may be indicative of the likelihood that an HPV infection will progress to carcinoma. To detect an HPV mRNA by the method of the present invention, the mRNA can be treated with reverse transcriptase in an appropriate reaction mixture to synthesize a cDNA molecule. The primer used in the reverse transcription reaction can be a consensus primer of the invention or can be a different oligonucleotide that hybridizes near the 3' end of the mRNA. Although random hexamers are not specific for the 3' end of the molecule, they are suitable for reverse transcription of RNA to provide a cDNA template for amplifying HPV nucleic acids. This cDNA copy is then made into a double stranded DNA molecule, which can be detected and typed in accordance with the method of the present invention.

The present invention may be assembled as a kit for detecting and typing HPV. Such a kit would include consensus primers and type-specific probes. A preferred kit also includes means for determining if amplification has occurred, such as a consensus probe or long probe. Additional kit components may include and am not limited to any of the following: PCR buffers and enzymes; positive control HPV or non-HPV DNAs; positive control primers, for example, β-globin primers; a positive control probe; primers for preparing long probes; means for detecting hybridized probes; and instructions for amplifying, detecting, and typing HPV.

Those skilled in the art recognize that the specific primers and probes disclosed herein are merely illustrative of the invention. For instance, because the primers and many of the probes of the invention are single-stranded DNA molecules, and because the target DNA (HPV DNA in a sample) is double-stranded DNA, useful primers and probes of the invention can be constructed merely by synthesizing primers and probes complementary to those specifically disclosed herein. The primers and probes of the invention can also be prepared to amplify and detect sequence variations within areas of HPV genomes other than those specifically exemplified herein.

The methods of the present invention, although applicable to any HPV, are exemplified below with reference to genital and dermal HPV types. Furthermore, primers and probes can be targeted to areas of the HPV genome other than those described below, provided that the particular area targeted can be amplified using consensus primers and the amplified DNA can be typed using type-specific probes.

Throughout the specification nucleotides are designated as follows.

    ______________________________________                                         Symbol Meaning      Origin                                                     ______________________________________                                         G      G            Guanine                                                    A      A            Adenine                                                    T      T            Thymine                                                    C      C            Cytosine                                                   R      G or A       puRine                                                     Y      T or C       pYrimidine                                                 M      A or C       aMino                                                      K      G or T       Keto                                                       S      G or C       Strong interaction (3 H bonds)                             W      A or T       Weak interaction (2 H bonds)                               H      A or C or T  not-G, H follows G in the alphabet                         B      G or T or C  not-A, B follows A                                         V      G or C or A  not-T (not-U), V follows U                                 D      G or A or T  not-C, D follows C                                         N      G or A or T or C                                                                            aNy                                                        ______________________________________                                    

L1E6 Region

In one embodiment, the L1/E6 consensus primer combinations of the invention are designed to amplify a sequence of DNA from any genital HPV. The amplified sequence extends from L 1 across the URR and into E6 and thus contains portions of the L 1 and E6 regions with the URR region sandwiched in between the L 1 and E6 regions. Thus, the consensus primer pairs consist of a first primer specific for a sequence in the L 1 region and a second primer specific for a sequence in the E6 region. As shown in Table 1, below, the first L1-specific primer can be either FS10 (Seq ID No. 21), FS17 (Seq ID No. 264), or MY01 (Seq ID No. 263), while the second, E6-specific primer is at least a 1:1 mixture of JS15 and JS16 (Seq ID Nos. 265 and 266), although the mixture can also contain more JS15 than JS16 (Seq ID Nos. 265 and Table 1 also depicts the sequence of each primer and the corresponding sequence (and nucleotide position of that sequence) as it occurs in the genomes of several well-known genital HPVs (Types 6, 11, 16, 18, and 33). A dash in a sequence indicates that the genomic sequence is identical to the primer sequence.

                                      TABLE 1                                      __________________________________________________________________________     L1/E6 Consensus Primers and Amplification Products                             L1 Consensus Positive Strand Primers                                           __________________________________________________________________________     FS10 (Seq ID No. 21)                                                                       C T G T G G T A G A T A C C A C A C G C A G T A C                  HPV06 6770  --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --      --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                 HPV11 6756  --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --      --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                 HPV16 6633  --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --      --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                 HPV18 6587  --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --      --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                 HPV33 6587  --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --      --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                 FS17 (Seq ID No. 264)                                                                      5'                                                                               G A T C A G T T T C C Y Y T K G G       A                                                                              C                                                                              G                        MY01 (Seq ID No. 263)                                                                      5'                                                                               G A T C A G T W T C C Y Y T K G G       A                                                                              C                                                                              G                        HPV06 7151    --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               T T --                                                                               G --                                                                               --      --                                                                             --                                                                             --                       HPV11 7136    --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               C C --                                                                               T --                                                                               --      --                                                                             --                                                                             --                       HPV16 7015    --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               T T --                                                                               A --                                                                               --      --                                                                             --                                                                             --                       HPV18 6993    --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               A --                                                                               --                                                                               --                                                                               C C --                                                                               T --                                                                               --      --                                                                             --                                                                             --                       HPV33 6968    --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               T T --                                                                               G --                                                                               --      --                                                                             --                                                                             --                       __________________________________________________________________________     URR/E6 Consensus Negative Strand Primer                                        __________________________________________________________________________     JS15 (Seq ID No. 265)                                                                            5'                                                                               C C G T T T T C G G T   T S A A C C G                      HPV06 60            --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --  --                                                                               G --                                                                               --                                                                               --   --                                                                        --                         HPV11 60            --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --  --                                                                               G --                                                                               --                                                                               --   --                                                                        --                         HPV16 60            --                                                                               --                                                                               --                                                                               G --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --  --                                                                               C --                                                                               --                                                                               --   --                                                                        --                         HPV33 64            --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --  --                                                                               G --                                                                               --                                                                               --   --                                                                        --                         JS16 (Seq ID No. 266)                                                                            5'                                                                               C C G T T T T C G G T C C C G A C    C                                                                         G                          HPV18 68            --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --   --                                                                        --                         __________________________________________________________________________     Predicted Sizes Of PCR Products                                                __________________________________________________________________________     +PRIMER           FS10 (Seq ID No. 21)  FS17 or MY01 (Seq ID                                                           Nos. 264 and 263)                      PRIMER            JS15 and JS16 (Seq ID JS15 and JS16 (Seq ID                                    Nos. 265 and 266)     Nos. 265 and 266)                      HPV06             1192 bp               822 bp                                 HPV11             1235 bp               856 bp                                 HPV16             1387 bp               958 bp                                 HPV18             1367 bp               932 bp                                 HPV33             1434 bp               1005 bp                                __________________________________________________________________________

As shown in Table 1, FS10 (Seq ID No. 21) is a 25-mer that has 3 mismatches with HPV16 and 1 mismatch with HPV18 and HPV33. FS17 (Seq ID No. 264) is a degenerate primer with 1 or 2 mismatches to different HPVs. MY01 (Seq ID No. 263) is similar to FS17 (Seq ID No. 264), contains 1 more degenerate base to decrease mismatches and to potentially cover a wider range of HPVs. JS15 (Seq ID No. 265) is a degenerate 18-mer for the negative strand in E6 of HPVs 6, 11, 16, and 33, whereas JS16 (Seq ID No. 266) is a 19-mer serving the same function for HPV18.

Once a sample has been treated with the L1/E6 primers shown above under conditions suitable for PCR, the method of the invention requires the determination of whether amplification has occurred. If amplification has occurred with the L1/E6 primers, HPV sequences are present in the sample. In one aspect of the invention, a consensus probe is used to determine if amplification has occurred. Alternatively, amplification of HPV DNA using the L1/E6 consensus primers FS10 (Seq ID No. 21), JS15 (Seq ID No. 265), and JS16 (Seq ID No. 266) can be detected using the L1/E6 consensus primer FS17 (Seq ID No. 264) or MY01 (Seq ID No. 263).

The present invention provides a number of type-specific probes for use with the L1/E6 consensus primers of the invention. These probes are set forth in Table 2, below. Those skilled in the art will recognize that although the specific primers and probes of the invention exemplified herein have a defined number of nucleotide residues, one or more nucleotide residues may be added or deleted from a given primer or probe typically without great impact on the suitability of that primer or probe in the present methods.

                                      TABLE 2                                      __________________________________________________________________________     HPV Typing Probes For Use with L1/E6 Consensus Primers                               Sequence                                                                 Specificity                                                                          ID No.                                                                              Sequence            Size Designation                                __________________________________________________________________________     HPV6  1    5'CCAAACAGTAAGAGC   (15-mer)                                                                            FS18                                       HPVll 2    5'GGCTGTAGAGGGCTTAGAC                                                                              (19-mer)                                                                            FS19                                       HPV16 3    5'GGTTGAAGCTACAAAATGGGCC                                                                           (22-mer)                                                                            JS17                                       HPV18 4    5'GTAGCGCACCTGGACAGG                                                                               (18-mer)                                                                            FS21                                       HPV33 5    5'CAGGTAGTGACTCAC   (15-mer)                                                                            FS22                                       __________________________________________________________________________

FS19 (Seq ID No. 2) and JS17 (Seq ID No. 3) can specifically detect HPV11 and HPV16, respectively. FS18 (Seq ID No. 1 ) shows some hybridization with the HPV 11 PCR product. UWGCG GAP program analysis comparing FS18 (Seq ID No. 1) sequence and HPV 11 sequence indicates a 73% homology of FS18 (Seq ID No. 1 ) to HPV 11 in the amplified region. The cross-hybridization could be minimized by increasing the stringency of washing. FS21 (Seq ID No. 4) was specific for HPV 18.

L1 Region

The L1/E6 primers disclosed above provide for the amplification of relatively large segments of HPV DNA. However, use of primers that result in shorter PCR products can have several advantages, including reduced extension and denaturation time and decreased denaturation temperature. The L1 consensus primers of the invention are illustrative of primers designed to amplify relatively small segments of the HPV genome to achieve such advantages. The L1 consensus primers, MY11 (Seq ID No. 267), MY09 (Seq ID No. 269), PEG01 (Seq ID No. 268), and PEG02 (Seq ID No. 270), amplify a region of the L1 open reading frame and are depicted in Table 3, below.

                                      TABLE 3                                      __________________________________________________________________________     L1 Consensus Primers and Amplification Products                                L1 Consensus Positive Strand Primers                                           __________________________________________________________________________     MY11 (Seq ID No. 267)                                                                       5'                                                                               G C M C A G G G W C A T A A Y A A T G G                         PEG01 (Seq ID No. 268)                                                                      5'                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               D --                                                                               --                                                                               Y --                                                                               --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                       HPV06 6722     --                                                                               --                                                                               C --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               C --                                                                               --     --                                                                      --     --                       HPV11 6707     --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               C --                                                                               --     --                                                                      --     --                       HPV16 6584     --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               C --                                                                               --                                                                               C --                                                                               --                                                                               T --                                                                               --     --                                                                      --     --                       HPV18 6558     --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               C --                                                                               --     --                                                                      --     --                       HPV31          --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               C --                                                                               --                                                                               T --                                                                               --     --                                                                      --     --                       HPV33 6539     --                                                                               --                                                                               A --                                                                               --                                                                               A --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --     --                                                                      --     --                       __________________________________________________________________________     L1 Consensus Negative Strand Primers                                           __________________________________________________________________________     MY09 (Seq ID No. 269)                                                                       5'                                                                               C G T C C M A R R G G A W A C T G A  T                                                                               C                         PEG02 (Seq ID No. 270)                                                                      5'                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               Y --                                                                               --     --                                                                      --     --                       HPV06 7171     --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               C --                                                                               A A --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                       HPV11 7155     --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               G G --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                       HPV16 7035     --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               A A --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                       HPV18 7012     --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               G G --                                                                               --                                                                               --                                                                               T --                                                                               T --                                                                               --     --                                                                      --     --                       HPV31          --                                                                               --                                                                               A --                                                                               --                                                                               C --                                                                               G T --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                       HPV33 6988     --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               C --                                                                               A A --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                       HPV54          --                                                                               --                                                                               A --                                                                               --                                                                               A --                                                                               --                                                                               G --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --     G                                                                       --     --                       __________________________________________________________________________     Predicted sizes of PCR products from the                                       MY11 (Seq ID No. 267) and MY09 (Seq ID No. 269)                                Consensus Primer Pair                                                          __________________________________________________________________________     HPV06        448 bp                                                            HPV11        448 bp                                                            HPV16        451 bp                                                            HPV18        454 bp                                                            HPV33        448 bp                                                            __________________________________________________________________________

PEG01 (Seq ID No. 268) and PEG02 (Seq ID No. 270) are modifications of MY11 (Seq ID No. 267) and MY09 (Seq ID No. 269) which amplify the various HPV types with more uniform efficiency. A uniform amplification efficiency allows the detection of the various HPV types with a uniform sensitivity.

The methods of the present invention are useful for detecting any HPV DNA. A preferred embodiment of the HPV typing methods of the present invention comprises amplification of HPV sequences, if present in the sample, with the L1 consensus primers MY09 (Seq ID No. 269) and MY11 (Seq ID No. 267); determination of amplification by hybridization of a portion of the PCR reaction mixture with a generic HPV long probe; and finally, type determination with type-specific probes. This embodiment is useful for detecting and typing nucleic acids of both dermal and genital HPVs including genital HPV types 6, 11, 16, 18, 26, 30, 31, 33, 35, 39, 40, 42, 43, 45, 51, 52, 53, 54, 55, 57, 58, and 59, as well as dermal HPV types 5, 8, 27, 41, 47, and 48. At present, more than 60 unique HPV types have been identified. These are briefly described in deVilliers, 1989, J. Virol. 63:4898. The present invention is useful for typing known HPV types as well as identifying unique types or variants. To determine if amplification of HPV DNA sequences has occurred in a sample that has been treated with the L1 consensus primers of the invention, a portion of the PCR reaction mixture can be hybridized with L1 consensus probes, depicted in Table 4. Additional L1 consensus probes are provided below and in Example 8.

                                      TABLE 4                                      __________________________________________________________________________     L1 Consensus Probes                                                            __________________________________________________________________________     FS10 (Seq ID No.                                                                          5'                                                                               C T G T G G T A G A T A C C A C A C G C A G T A C                 21)                                                                            MY18 (Seq ID No.                                                                          5'                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --      --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                                                                               --                106)                                                                           MY19 (Seq ID No.                                                                          5'                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T       --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                                                                               --                271)                                                                           __________________________________________________________________________     Sequence of HPV types in Region of Consensus Probe                             __________________________________________________________________________     HPV6 6771  5'                                                                               C T  G                                                                               T G G T A G A T A C C A C A C G C A G T A C                 HPV11 6756 5'                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --      --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                                                                               --                HPV16 6631 5'                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --      --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                                                                               --                HPV18 6607 5'                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T       --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                                                                               --                HPV33 6588 5'                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T       --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                                                                               --                Isolate 36 5'                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               G --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               C       A                                                                              --                                                                             A                                                                              --                                                                               --                                                                               C --                                                                               --                Isolate 88 5'                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               T       --                                                                             --                                                                             --                                                                             --                                                                               --                                                                               C --                                                                               --                __________________________________________________________________________

As noted above, the diversity of HPV types may mandate the use of longer consensus probes that contain almost all of the amplified sequence except that portion corresponding to the primers used in the amplification step of the present method. This diversity in HPV types also demonstrates the need for the type-specific probes provided by the present invention. In a preferred embodiment, the method utilizes a generic probe comprising PCR fragments. The PCR fragments provide long probes for the use as consensus probes for determining if amplification has occurred. According to Example 1, a generic probe was synthesized from the 450 base pair L1 PCR fragments of HPV-16, HPV-18, and the highly divergent isolates PAP88 and PAP238B. The generic probe described in Example 1 comprises segments approximately 400 base pairs in length and can be prepared using the primers depicted below. The primers are used in pairs corresponding to the target; i.e., MY74 (Seq ID No. 6) and MY75 (Seq ID No. 7) for HPV16, MY76 (Seq ID No. 8) and MY77 (Seq ID No. 9) for HPV18, MY47 (Seq ID No. 10) and MY48 (Seq ID No. 11) for PAP88, and MY49 (Seq ID No. 12) and MY50 (Seq ID No. 13) for PAP238B. An alternate generic probe is described in Example 4, below.

    ______________________________________                                         Internal PCR Primers for Generic Probe                                               Seq                                                                            ID                                                                       Name  No.    Sequence              Target                                      ______________________________________                                         MY74   6     CATTTGTTGGGGTAACCAAC  HPV 16                                      MY75   7     TAGGTCTGCAGAAAACTTTTC HPV 16                                      MY76   8     TGTTTGCTGGCATAATCAAT  HPV 18                                      MY77   9     TAAGTCTAAAGAAAACTTTTC HPV 18                                      MY47  10     CATATGCTGGGGTAATCAGG  PAP 88                                      MY48  11     CAGGTCTGCAGAAAAGCTGT  PAP 88                                      MY49  12     TATTTGTTGGGGCAATCAG   PAP 238B                                    MY50  13     CTAAATCTGCAGAAAACTTTT PAP 238B                                    ______________________________________                                    

Practice of the present invention has led to the discovery of many previously uncharacterized HPV types. These new sequences are an important aspect of the present invention, as are the probes that will hybridize to these sequences in a type-specific fashion. These new sequences are depicted below. Degenerate nucleotides are as defined above and correspond to the degenerate nucleotides in the primers used to amplify the region or to variation within the type.

    __________________________________________________________________________     The DNA Sequences of the L1 Amplified Regions of HPV                           __________________________________________________________________________     Isolates 36A - Seq. ID No. 14                                                  1  GCMCAGGGWC                                                                               ATAAYAATGG                                                                               TATATGTTGG                                                                               CACAATCAAT                                                                               TGTTTTTAAC                          51 AGTTGTAGAT                                                                               ACTACTCGCA                                                                               GCACCAATCT                                                                               YTCTGTGTGT                                                                               GCTTCTACTA                          101                                                                               CTTCTCCTAT                                                                               TCCTAATGAA                                                                               TACACACCTA                                                                               CCAGTTTTAA                                                                               AGAATATGCC                          151                                                                               AGACATGTGG                                                                               RGGAATTTGA                                                                               TTTGCAGTTT                                                                               ATAYTTCAAC                                                                               TGTGTAAAAT                          201                                                                               AACWTTAACT                                                                               ACAGAGGTAA                                                                               TGTCATACAT                                                                               TCATAATATG                                                                               AATACCACTA                          251                                                                               TTTTGGAGGA                                                                               TTGGAATTTT                                                                               GGTRTTACAC                                                                               CACCTCCTAC                                                                               TGCTARTTTA                          301                                                                               GTTGACACAT                                                                               ACCGTTTTGT                                                                               TCAATCTGCT                                                                               GCTGTAACTT                                                                               GTCAAAAGGA                          351                                                                               CACCGCACCG                                                                               CCAGTTAAAC                                                                               AGGACCCTTA                                                                               TGACAAACTA                                                                               AAGTTTTGGA                          401                                                                               CTGTAAATCT                                                                               TAAGGAAAGG                                                                               TTTTCTGCAG                                                                               ATCTTGATCA                                                                               GTWTCCYYTK                          451                                                                               GGACG                                                                       Isolate 36B - Seq ID No. 15                                                    1  GCMCAGGGWC                                                                               ATAAYAATGG                                                                               TATATGTTGG                                                                               GGAAATCAGC                                                                               TATTTTTAAC                          51 TGTGGTTGAT                                                                               ACTACCCGTA                                                                               GTACTAACAT                                                                               GACTTTGTGY                                                                               GCCACTGCAA                          101                                                                               CATCTGGTGA                                                                               TACATATACA                                                                               GCTGCTAATT                                                                               TTAAGGAATA                                                                               TTTAAGACAT                          151                                                                               GCTGAAGAAT                                                                               ATGATGTGCA                                                                               ATTTATATTT                                                                               CAATTGTGTR                                                                               AAATAACATT                          201                                                                               AACTGTTGAA                                                                               GTTATGTCAT                                                                               ATATACACAA                                                                               TATGAATCCT                                                                               AACATATTAG                          251                                                                               AGGAGTGGAA                                                                               TGTTGGTGTT                                                                               GCACCACCAC                                                                               CTTCAGGAAC                                                                               TTTAGAAGAT                          301                                                                               AGTTATAGGT                                                                               ATGTACAATC                                                                               AGAAGCTATT                                                                               CGCTGTCAGG                                                                               CTAAGGTAAC                          351                                                                               AACGCCAGAA                                                                               AAAAAGGATC                                                                               CTTATTCAGA                                                                               CTTTTCCTTT                                                                               TGGGAGGTAA                          401                                                                               ATTTATCTGA                                                                               AAAGTTTTCT                                                                               ACTGATTTAG                                                                               GATCAGTWTC                                                                               CYYTKGGACG                          Isolate 88 - Seq ID No. 16                                                     1  GCMCAGGGWC                                                                               ATAAYAATGG                                                                               CATATGCTGG                                                                               GGTAATCAGG                                                                               TATTTGTTAC                          51 TGTTGTGGAT                                                                               ACTACCAGAA                                                                               GCACCAACAT                                                                               GACTATTAAT                                                                               GCAGCTAAAA                          101                                                                               GCACATTARC                                                                               TAAATATGAT                                                                               GCCCGTGAAA                                                                               TCAATCAATA                                                                               CCTTCGCCAT                          151                                                                               GTGGAGGAAT                                                                               ATGAACTACA                                                                               GTTTGTGTTT                                                                               CAACTTTGTA                                                                               AAATAACCTT                          201                                                                               AACTGCAGAR                                                                               GTTATGGCAT                                                                               ATTTGCATAA                                                                               TATGAATAAT                                                                               ACTTTATTRG                          251                                                                               ACGATTGGAA                                                                               TATTGGCTTA                                                                               TCCCCACCAG                                                                               TTGCAACTAG                                                                               CTTAGAGGAT                          301                                                                               AAATATAGGT                                                                               ATATTAAAAG                                                                               CACAGCTRTT                                                                               ACAYGTCAGA                                                                               GGGAACAGCC                          351                                                                               CCCTGCAGAA                                                                               AAGCAGGATC                                                                               CCCTGGCTAA                                                                               ATATAAGTTT                                                                               TGGGAAGTTA                          401                                                                               ATTTACAGGA                                                                               CAGCTTTTCT                                                                               GCAGACCTGG                                                                               GATCAGTWTC                                                                               CYYTKGGACG                          Isolate 238A - Seq ID No. 17                                                   1  GCMCAGGGWC                                                                               ATAAYAATGG                                                                               TATTTGTTGG                                                                               CATAATCART                                                                               TATTTTTAAC                          51 TGTTGTAGAT                                                                               ACTACTAGAA                                                                               GCACTAATTT                                                                               TTCTGTATGT                                                                               GTAGGTACAC                          101                                                                               AGGCTAGTAG                                                                               CTCTACTACA                                                                               ACGTATGCCA                                                                               ACTCTAATTT                                                                               TAAGGAATAT                          151                                                                               TTAAGACATG                                                                               CAGAAGAGTT                                                                               TGATTTACAG                                                                               TTTGTTYTTC                                                                               AGTTATGTAA                          201                                                                               AATTAGTTTA                                                                               ACTACTGAGG                                                                               TAATGACATA                                                                               TATACATTCT                                                                               ATCAATTCTA                          251                                                                               CTATATTGGA                                                                               AGAGTGGAAT                                                                               TTTGGTCTTA                                                                               CCCCACCACC                                                                               OTCAGGTACT                          301                                                                               TTAGAGGAAA                                                                               CATATAGATA                                                                               TGTAACATCA                                                                               CAKGCTATTA                                                                               GTTGCCAACG                          351                                                                               TCCTCAACCT                                                                               CCTAAAGAAA                                                                               CAGAGGACCC                                                                               ATATGCCAAG                                                                               CTATCCTTTT                          401                                                                               GGGATGTAGA                                                                               TCTTAAGGAA                                                                               AAGTTTTCTG                                                                               CAGAATTAGA                                                                               TCAGTWTCCY                          451                                                                               YTKGGACG                                                                    Isolate 238B - Seq ID No. 18                                                   1  GCMCAGGGWC                                                                               ATAAYAATGG                                                                               TATTTGTTGG                                                                               GGCAATCAGT                                                                               TATTTGTTAC                          51 TGTGGTAGAT                                                                               ACCACACGTA                                                                               GTACCAATAT                                                                               GTCTGTGTGT                                                                               GCTGCAATTG                          101                                                                               CAAACAGTGA                                                                               TACTACATTT                                                                               AAAAGTAGTA                                                                               ATTTTAAAGA                                                                               GTATTTAAGA                          151                                                                               CATGGTGAGG                                                                               AATTTGATTT                                                                               ACRATTTATA                                                                               TTTCAGTTAT                                                                               GCAAAATAAC                          201                                                                               ATTATCTGCA                                                                               GACATAATGA                                                                               CATATATTCA                                                                               CAGTATGAAT                                                                               CCTGCTATTT                          251                                                                               TGGAAGATTG                                                                               GAATTTTGGA                                                                               TTGACCACAC                                                                               CTCCCTCAGG                                                                               TTCTTTAGAG                          301                                                                               GATACCTATA                                                                               GGTTTGTAAC                                                                               CTCACAGGCC                                                                               ATTACATGTC                                                                               AAAAARCTGC                          351                                                                               CCCCCAAAAG                                                                               CCCAAGGAAG                                                                               ATCCATTTAA                                                                               AGATTATGTA                                                                               TTTTGGGAGG                          401                                                                               TTAATTTAAA                                                                               AGAAAAGTTT                                                                               TCTGCAGATT                                                                               TAGATCAGTW                                                                               TCCYYTKGGA                          451                                                                               CG                                                                          Isolate 155A and 155B - Seq ID No. 19                                          1  TATATGCTGG                                                                               TTTAATCAAT                                                                               TGTTTGTCAC                                                                               GGTGGTGGAT                                                                               ACCACCCGCA                          51 GCACCAATIT                                                                               TACTATTAGT                                                                               GCTGCTACCA                                                                               ACACCGAATC                                                                               AGAATATAAA                          101                                                                               CCTACCAATT                                                                               TTAAGGAATA                                                                               CCTAAGACAT                                                                               GTGGAGGAAT                                                                               ATGATTTGCA                          151                                                                               GTTTATATTC                                                                               CAGTTGTGTA                                                                               AGGTCCGTCT                                                                               GACTCCAGAG                                                                               GTCATGTCCT                          201                                                                               ATTTACATAC                                                                               TATGAATGAC                                                                               TCCTTATTAG                                                                               ATGAGTGGAA                                                                               TTTTGGTGTT                          251                                                                               GTGCCCCCTC                                                                               CCTCCACAAG                                                                               TTTAGATGAT                                                                               ACCTATAGGT                                                                               ACTTGCAGTC                          301                                                                               TCGCGCCATT                                                                               ACTTGCCAAA                                                                               AGGGGGCCGC                                                                               CGCCGCCAAG                                                                               CCTAAGGAAG                          351                                                                               ATCCTTATGC                                                                               TGGCATGTCC                                                                               TTTTGGGATG                                                                               TAGATTTAAA                                                                               GGACAAGTTT                          401                                                                               TCTACTGATT                                                                               TG                                                                Isolate C14 - Seq ID No. 20                                                    1  TATTTGTTGG                                                                               CATAATCAGT                                                                               TGTTTGTTAC                                                                               TGTAGTGGAC                                                                               ACTACCCGCA                          51 GTACTAATTT                                                                               AACATTATGT                                                                               GCCTCTACAC                                                                               AAAATCCTGT                                                                               GCCAAATACA                          101                                                                               TATGATCCTA                                                                               CTAAGTTTAA                                                                               GCACTATAGT                                                                               AGACATGTGG                                                                               AGGAATATGA                          151                                                                               TTTACAGTTT                                                                               ATTTTTCAGT                                                                               TGTGCACTAT                                                                               TACTTTAACT                                                                               GCAGAGGTTA                          201                                                                               TGTCATATAT                                                                               CCATAGTATG                                                                               AATAGTAGTA                                                                               TATTGGAAAA                                                                               TTGGAATTTT                          251                                                                               GGTGTACCTC                                                                               CACCACCTAC                                                                               TACAAGTRRA                                                                               GTGGATACAT                                                                               ATCGTTTTGT                          301                                                                               GCAATCCGTT                                                                               GCTGTTACCT                                                                               GTCAAAAGGA                                                                               TACTACACCT                                                                               CCAGAAAAGC                          351                                                                               AGGATCCATA                                                                               TGATAAATTA                                                                               AAGTTTTGGA                                                                               CTGTTGACCT                                                                               AAAGGAAAAA                          401                                                                               TTTTCCTCCG                                                                               ATTTG                                                             Isolate B6062 - Seq ID No. 273                                                 1  GAGCTCGCAC                                                                               AGGGTCATAA                                                                               CAATGGTATC                                                                               TGTTGGGGCA                                                                               ATCAATTGTT                          51 TGTTACCTGT                                                                               GTTGATACCA                                                                               CCCGCAGTAC                                                                               TAACCTTACC                                                                               ATTAGTACAT                          101                                                                               TATCTGCAGC                                                                               ATCTGCATCC                                                                               ACTCCATTTA                                                                               AACCATCTGA                                                                               TTATAAACAA                          151                                                                               TTTATAAGAC                                                                               ATGGCGAAGA                                                                               ATATGAATTA                                                                               CAATTTATAT                                                                               TTCAGTTCTG                          201                                                                               TAAAATAACA                                                                               CTTACAACAG                                                                               ATGTTATGGC                                                                               TTACATACAT                                                                               TTAATGAATG                          251                                                                               CCTCCATATT                                                                               GGAGGATTGG                                                                               AATTTTGGAC                                                                               TAACCTTACC                                                                               TCCCACTGCT                          301                                                                               AGTTTGGAAG                                                                               ATGCCTATAG                                                                               GTTTATTAAA                                                                               AACTCTGCTA                                                                               CTACCTGTCA                          351                                                                               GCGTAACGCC                                                                               CCTCCTGTGC                                                                               CAAAGGAAGA                                                                               TCCTTTTCAA                                                                               AAATTTAAAT                          401                                                                               TTTGGGATGT                                                                               AGATTTAAAA                                                                               GAAAAATTTT                                                                               CTATTGATTT                                                                               GGATCAGTTT                          451                                                                               CCCCTGGGAC                                                                               GAAGCTT                                                           Isolate D3173 - Seq ID No. 274                                                 1  GAGCTCGCCC                                                                               AGGGTCATAA                                                                               TAATGGCATC                                                                               TGTTGGAACA                                                                               ATCAGTTATT                          51 TGTAACTGTT                                                                               GTGGATACCA                                                                               CCAGGAATAC                                                                               AAACATGACA                                                                               CTTTCTGCAA                          101                                                                               CCACACAGTC                                                                               TATGTCCACA                                                                               TATAATTCAA                                                                               AGCAAATTAA                                                                               ACAGTATGTT                          151                                                                               AGACATGCAG                                                                               AGGAATATCA                                                                               ATTACAATTT                                                                               GTGTTTCAAC                                                                               TATGTAAAAT                          201                                                                               ATCCCTGTCT                                                                               GCTGAGGTTA                                                                               TGGCCTATTT                                                                               ACATACTATG                                                                               AATTCTACCT                          251                                                                               TACTGGAAGA                                                                               CTGGAATATA                                                                               GGTTTGTCGC                                                                               CTCCTGTTGC                                                                               CACTAGCTTA                          301                                                                               GAGGACAAAT                                                                               ACAGATATGT                                                                               AAAAAGTGCA                                                                               GCTATAACCT                                                                               GTCAAAAGGA                          351                                                                               TCAGCCCCCT                                                                               CCTGAAAAGC                                                                               AGGACCCACT                                                                               ATCTAAATAT                                                                               AIATTTTGGG                          401                                                                               AGGTCAATTT                                                                               ACAAAACAGT                                                                               TTTTCTGCTG                                                                               ATTTGGATCA                                                                               GTATCCCCTG                          451                                                                               GGACGAAGCT                                                                               T                                                                 Isolate 7552 - Seq ID No. 275                                                  1  GAGCTCGCCC                                                                               AGGCTCATAA                                                                               TAATGGTATT                                                                               TGTTGGTTTA                                                                               ATGAATTGTT                          51 TGTAACCGTT                                                                               GTGGATACCA                                                                               CCCGCAGTAC                                                                               TAATGTAACC                                                                               ATTTGTACTG                          101                                                                               CTACATCCCC                                                                               CCCTGTATCT                                                                               GAATATAAAG                                                                               CCACGAGCTT                                                                               TAGGGAATAT                          151                                                                               TTGCGCCATA                                                                               CAGAAGAGTT                                                                               TGATTTGCAA                                                                               TTCATTTTTC                                                                               AGTTATGTAA                          201                                                                               AATACATTTA                                                                               ACCCCTGAAA                                                                               TTATGGCCTA                                                                               CCTACATAAT                                                                               ATGAATAAAG                          251                                                                               CCTTGTTGGA                                                                               TGACTGGAAC                                                                               CTTGGTGTGG                                                                               TACCTCCACC                                                                               CTCTACCAGT                          301                                                                               CTAGAAGACA                                                                               CATATAGGTT                                                                               TTTGCAGTCC                                                                               AGAGCTATTA                                                                               CATGTCAGAA                          351                                                                               GGGTGCTGCT                                                                               GCCCCGCCGC                                                                               CCAAGGAGGA                                                                               TCGCTATGCC                                                                               AAATTATCAT                          401                                                                               TTTGGACTGT                                                                               TGATTTACGA                                                                               GACAAGTTCT                                                                               CCACTGATTT                                                                               GGATCAGTAT                          451                                                                               CCCTTGGGAC                                                                               GAAGCTT                                                           Isolate JB10 - Seq ID No. 276                                                  1  GAGCTCGCAC                                                                               AGGGACATAA                                                                               CAATGGCATT                                                                               TGTTGGGGCA                                                                               ACCAATTGTT                          51 TGTTACTTGT                                                                               GTAGATACTA                                                                               CCCGCAGTAC                                                                               CAACCTCACT                                                                               ATTAGTACTG                          101                                                                               TATCTGCACA                                                                               ATCTGCATCT                                                                               GCCACTTTTA                                                                               AACCATCAGA                                                                               TTATAAGCAG                          151                                                                               TTTATAAGGC                                                                               ATGGTGAGGA                                                                               ATATGAATTA                                                                               CAGTTTATAT                                                                               TTCAATTGTG                          201                                                                               TAAAATTACT                                                                               CTTACCACTG                                                                               ATGTAATGGC                                                                               CTATATCCAT                                                                               ACAATGAATT                          251                                                                               CTGCTATTTT                                                                               GGAAAATTGG                                                                               AATTTTGGCC                                                                               TTACCTTGCC                                                                               TCCTACTGCT                          301                                                                               AGTTTGGAAG                                                                               ATGCATATAG                                                                               GTTTATTAAA                                                                               AATTCAGCTA                                                                               CTACATGTCA                          351                                                                               ACGCGATGCC                                                                               CCTGCACAGC                                                                               CCAAGGAGGA                                                                               TCCATTTAGT                                                                               AAATTAAAAT                          401                                                                               TTTGGGACGT                                                                               TGATCTTAAA                                                                               GAAAAGTTTT                                                                               CTATTGATTT                                                                               AGATCAGTAT                          451                                                                               CCCCTTGGAC                                                                               GAAGCTT                                                           Isolate Lavc5 - Seq ID No. 277                                                 1  GAGCTCGCCC                                                                               AGGGTCATAA                                                                               TAATGGTCTT                                                                               TAAAAGTGAA                                                                               AGAGOGAGGC                          51 AGAAGAAGGT                                                                               GTGATAGTAT                                                                               AGGGATGTAA                                                                               AGAAGACTCA                                                                               ACCAGCCCTT                          101                                                                               GCTGGTTTTG                                                                               AAGCTGGAAG                                                                               AGGGTCGTGA                                                                               GCCAAGGAAT                                                                               AAGGGCAGCC                          151                                                                               TCTAAAAAGC                                                                               TGGAAAAGAT                                                                               CAGAAAATGG                                                                               TTCTCACCTA                                                                               CAGTCTCCAG                          201                                                                               AAAGGAACAC                                                                               CGTCTGGCCA                                                                               ACACCTTGAT                                                                               CTTAGCCCAG                                                                               TGAGACTCAT                          251                                                                               TTCTACCTTC                                                                               TGACTTCCAG                                                                               AAGTTTAAGG                                                                               TAATCAACTT                                                                               TTGTTGTTTT                          301                                                                               AAGCCACTGA                                                                               GTTAATGGCA                                                                               ATTTGTTACA                                                                               ACAGCCATAG                                                                               CAAGCTAGTA                          351                                                                               TACCGAGTCT                                                                               CATTCTTACC                                                                               CTTATGAGAC                                                                               CTTCCACAAT                                                                               TTCATCCCAT                          401                                                                               CCAACCCACC                                                                               CAGCAATGTC                                                                               TTCTGCTTGG                                                                               GTCAGATCAG                                                                               TATCCCTTTG                          451                                                                               GACGAAGCTT                                                                  Isolate D7515 - Seq ID No. 278                                                 1  GAGCTCGCAC                                                                               AGGGACATAA                                                                               TAATGGTATA                                                                               TGCTGGGGTA                                                                               ATCAACTATT                          51 TGTTACTGTT                                                                               GTAGACACTA                                                                               CACGTAGTAC                                                                               CAACATGACT                                                                               TTATGTTCTG                          101                                                                               AGGAAAAATC                                                                               AGAGGCTACA                                                                               TACAAAAATG                                                                               AAAACTTTAA                                                                               GGAATACCTT                          151                                                                               AGACATGTGG                                                                               AAGGATATGA                                                                               TTTGCAGTTT                                                                               ATATTTCAGC                                                                               TGTGCAAAAT                          201                                                                               ATCCCTTACT                                                                               GCAAATGTTA                                                                               TGCAATACAT                                                                               ACACACCATG                                                                               AATCCAGATA                          251                                                                               TATTAGAGGA                                                                               CTGGCAATTT                                                                               GGCCTTACAC                                                                               CACCTCCTTC                                                                               AGGTAATTTA                          301                                                                               CAGGACACAT                                                                               ATAGATTTGT                                                                               TACCTCGCAG                                                                               GCTATTACCT                                                                               GTCAAAAAAC                          351                                                                               ATCCCCTCCA                                                                               ACAGCAAAGG                                                                               AAGATCCTCT                                                                               TAAAAAGTAC                                                                               AGTTTTTGGG                          401                                                                               AAATCAATTT                                                                               AAAGGAAAAA                                                                               TTTTCTGCAG                                                                               ATTTAGATCA                                                                               GTATCCCCTT                          451                                                                               GGACGAAGCT                                                                               T                                                                 Isolate Pap116 seq ID No. 279                                                  1  ACACTACACG                                                                               TAGTACTAAT                                                                               TTACATTGTC                                                                               TGCCTGCACC                                                                               GAAACAGCCG                          51 TACCTGCTGT                                                                               ATATAGCCCT                                                                               ACAAAGTTTA                                                                               AGGAATATAC                                                                               TAGGCATGTG                          101                                                                               GAGGAATATG                                                                               ATTTACAATT                                                                               TATATTTCAA                                                                               TTGTGTACTA                                                                               TCACATTAAC                          151                                                                               TGCAGACGTT                                                                               ATGGCCTACA                                                                               TCCATACTAT                                                                               GAATCCTACA                                                                               ATTTTGGACA                          201                                                                               ATTGGAATAT                                                                               AGGCGTTACC                                                                               CCTCCACCAT                                                                               CTGCAAGCTG                                                                               AGCTTGGTGG                          251                                                                               ACACGTATAG                                                                               GTATTTACAA                                                                               TCAGCAGCAT                                                                               AGCATGTCAG                                                                               AAGGATGCTC                          301                                                                               CTGCACCTGA                                                                               AAAAAAGGGT                                                                               CCCTATGACG                                                                               ATTTAAAATT                                                                               TTGGAATGTT                          351                                                                               GATTTAAAGG                                                                               AAAAGTTTAG                                                                               TAACAGAACT                                                                               AGATCAGTAT                                                                               CCCC                                Isolate W13b - Seq ID No. 280                                                  1  GAGCTCGCAC                                                                               AGGGACATAA                                                                               TAATGGCATT                                                                               TCGTGGAATA                                                                               ATCACGTTTT                          51 TATTACTTGT                                                                               GTTGACACTC                                                                               ATAGAATGAC                                                                               CAATTTAACC                                                                               ATTACGACTC                          101                                                                               GTGTTACTCA                                                                               ATCTGTTGCA                                                                               CAAACATTTA                                                                               CTCCAGCAAA                                                                               CTTTAAGCAA                          151                                                                               TACATTAGGC                                                                               ATGGGGAAGA                                                                               ATATCAATTG                                                                               CAATTTATAT                                                                               TTCAATTGTG                          201                                                                               TAAAATCACT                                                                               TTAACTACTG                                                                               AAATTATGGC                                                                               TTACCTGCAC                                                                               ACCATGGATT                          251                                                                               CTACAATTTT                                                                               AGAACAGTGG                                                                               AATTTTGGAT                                                                               TAACCTTGCC                                                                               CCCCTCAGCT                          301                                                                               AGTTTGGAGG                                                                               AGTCCTATGC                                                                               ATTTGTAAAA                                                                               AATGCAGCAA                                                                               CATCCTGTCA                          351                                                                               CAAGGACAGT                                                                               CCTCCACAGG                                                                               CTAAACAAGA                                                                               CCCTTTGGCA                                                                               AAATATAAAT                          301                                                                               TTTGGAATGT                                                                               AGACCTTAAG                                                                               GAAcGcTT7r                                                                               CTTTGGATTT                                                                               GGATCAGTTT                          351                                                                               CCTTTTGGAC                                                                               GAAGCTT                                                           Isolate Lavb24a - Seq ID No. 281                                               1  GAGCTCGCAC                                                                               AGGGGTCATA                                                                               ATAATGGCAT                                                                               ATGCTGGGGT                                                                               AATCAGGTAT                          51 TTGTTACTGT                                                                               TGTGGATACT                                                                               ACCAGAAGCA                                                                               CCAACATGAC                                                                               TATTAATGCA                          101                                                                               GCTAAAAGCA                                                                               CATTAACTAA                                                                               ATATGATGCC                                                                               CGTGAAATCA                                                                               ATCAATACCT                          151                                                                               TCGCCATGTG                                                                               GAGGAATATG                                                                               AACTACAGTT                                                                               TGTGTTTCAA                                                                               CCTTTGTAAAA                         201                                                                               TAACCTTAAC                                                                               TGCAGAAGTT                                                                               ATGGCATATT                                                                               TGCATAATAT                                                                               GAATAATACT                          251                                                                               TTATTAGACG                                                                               ATTGGAATAT                                                                               TGGATTATCC                                                                               CCACCAGTTG                                                                               CAACTAGCTT                          301                                                                               AGAGGATAAA                                                                               TATAGGTATA                                                                               TTAAAAGCAC                                                                               AGCTATTACA                                                                               TGTCAGAGGG                          351                                                                               AACAGCCCCC                                                                               TGCAGAAAAG                                                                               CAGGATCCCC                                                                               TGGCTAAATA                                                                               TAAGTTTTGG                          401                                                                               GAAGTTAATT                                                                               TACAGAACAG                                                                               CTTTTCTGCA                                                                               GACCTGGATC                                                                               AGTTTCCTTT                          451                                                                               TGGACGAAGC                                                                               TT                                                                Isolates Lavb24b and PAP291 - Seq ID No. 282                                   1  GAGCTCGCCC                                                                               AGGGACATAA                                                                               TAATGGCATT                                                                               TGTTGGTTTA                                                                               ATGAGTTATT                          51 TGTTACAGTT                                                                               GTAGATACTA                                                                               CCCGCAGTAC                                                                               CAATATTACT                                                                               ATTTCAGCTG                          101                                                                               CTGCTACACA                                                                               GGCTAATGAA                                                                               TACACAGCCT                                                                               CTAACTTTAA                                                                               GGAATACCTC                          151                                                                               CGCCACACCG                                                                               AGGAATATGA                                                                               CYYACCAGGTT                                                                              ATATTGCAAC                                                                               TTTGCAAAAT                          201                                                                               ACATCTTACC                                                                               CCTGAAATTA                                                                               TGGCATACCT                                                                               ACATAGTATG                                                                               AATGAACATT                          251                                                                               TATTGGATGA                                                                               GTGGAATTTT                                                                               GGCGTGTTAC                                                                               CACCTCCTTC                                                                               CACCAGCCTT                          301                                                                               GATGATACCT                                                                               ATCGCTATCT                                                                               GCAGTCCCGT                                                                               GCTATTACCT                                                                               GCCAAAAGGG                          351                                                                               TCCTTCCGCC                                                                               CCTGCCCCTA                                                                               AAAAGGATCC                                                                               TTATGATGGC                                                                               CTTGTATTTT                          401                                                                               GGGAGGTTGA                                                                               TTTAAAGGAC                                                                               AAACTATCCA                                                                               CAGATTTGGA                                                                               TCAGTATCCT                          451                                                                               TTGGGACGAA                                                                               GCTT                                                              Isolate B8988 - Seq ID No. 283                                                 1  GAGCTCGCAC                                                                               AGGGTCATAA                                                                               TAATGGTATT                                                                               TGTTGGCATA                                                                               ATCAATTATT                          51 TCTTACTGTT                                                                               GTGGATACCA                                                                               CTCGCAGTAC                                                                               CAATTTTACT                                                                               TTGTCTACTA                          101                                                                               CTACTGAATC                                                                               AGCTGTACCA                                                                               AATATTTATG                                                                               ATCCTAATAA                                                                               ATTTAAGGAA                          151                                                                               TATATTAGGC                                                                               ATGTTGAGGA                                                                               ATATGATTTG                                                                               CAATTTATAT                                                                               TTCAGTTGTG                          201                                                                               TACTATAACA                                                                               TTGTCAACTG                                                                               ATGTAATGTC                                                                               CTATATACAT                                                                               ACTATGAATC                          251                                                                               CTGCTATTTT                                                                               GGATGATTGG                                                                               AATTTTGGTG                                                                               TTGCCCCTCC                                                                               ACCATCTGCT                          301                                                                               AGTCTTGTAG                                                                               ATACATACCG                                                                               CTATCTGCAA                                                                               TCAGCAGCAA                                                                               TTACATGTCA                          351                                                                               AAAAGACGCC                                                                               CCTGCACCTA                                                                               CTAAAAAGGA                                                                               TCCATATGAT                                                                               GGCTTAAACT                          401                                                                               TTTGGAATGT                                                                               AAATTTAAAA                                                                               GAAAAGTTTA                                                                               GTTCTGAACT                                                                               GGATCAGTTT                          451                                                                               CCCCTTGGAC                                                                               GAAGCTT                                                           HPV35 (SEQ ID NO: 284)                                                         1  CAACGTGCAC                                                                               AAGGCCATAA                                                                               TAATGGTATT                                                                               TGTTGGAGTA                                                                               ACCAATTGTT                          51 TGTTACTGTA                                                                               GTTGATACAA                                                                               CCCGTAGTAC                                                                               AAATATGTCT                                                                               GTGTGTTCTG                          101                                                                               CTGTGTCTTC                                                                               TAGTGACAGT                                                                               ACATATAAAA                                                                               ATGACAATTT                                                                               TAAGGAATAT                          151                                                                               TTAAGGCATG                                                                               GTGAAGAATA                                                                               TGATTTACAG                                                                               TTTATTTTTTC                                                                              CAGTTATGTAA                         201                                                                               AATAACACTA                                                                               ACAGCAGATG                                                                               TTATGACATA                                                                               TATTCATAGT                                                                               ATGAACCCGT                          251                                                                               CCATTTTAGA                                                                               GGATTGGAAT                                                                               TTTGGCCTTA                                                                               CACCACCGCC                                                                               TTCTGGTACC                          301                                                                               TTAGAGGACA                                                                               CATATCGCTA                                                                               TGTAACATCA                                                                               CAGGCTGTAA                                                                               CTTGTCAAAA                          351                                                                               ACCCAGTGCA                                                                               CCAAAACCTA                                                                               AAGATGATCC                                                                               ATTAAAAAAT                                                                               TATACTTTTT                          401                                                                               GGGAGGTTGA                                                                               TTTAAAGGAA                                                                               AAGTTTTCTG                                                                               CAGACTTAGA                                                                               TCAATTTCCG                          451                                                                               TTGGGCCGTA                                                                               AATT                                                              HPV39 (SEQ ID NO: 285)                                                         1  GAGCTCGCCC                                                                               AGGGTCATAA                                                                               TAATGGTATA                                                                               TGTTGGCATA                                                                               ATCAATTATT                          51 TCTTACTGTT                                                                               GTGGACACTA                                                                               CCCGTAGTAC                                                                               CAACTTTACA                                                                               TTATCTACCT                          101                                                                               CTATAGAGTC                                                                               TTCCATACCT                                                                               TCTACATATG                                                                               ATCCTTCTAA                                                                               GTTTAAGGAA                          151                                                                               TATACCAGGC                                                                               ACGTGGAGGA                                                                               GTATGATTTA                                                                               CAATTTATAT                                                                               tTCAACTGTG                          201                                                                               TACTGTCACA                                                                               TTAACAACTG                                                                               ATGTTATGTC                                                                               TTATATTCAC                                                                               ACTATGAATT                          251                                                                               CCTCTATATT                                                                               GGaCAATTGG                                                                               AATTTTGCTG                                                                               TAGCTCCTCC                                                                               ACCATCTGCC                          301                                                                               AGTTTGGTAG                                                                               ACACTTACAG                                                                               ATACCTACAG                                                                               TCTGCAGCCA                                                                               TTACATGTCA                          351                                                                               AAAGGATGCT                                                                               CCAGCACCTG                                                                               AAAAGAAAGA                                                                               TCCATATGAC                                                                               GGTCTAAAGT                          401                                                                               TTTGGAATGT                                                                               TGACTTAAGG                                                                               GAAAAGTTTA                                                                               GTTTGGAACT                                                                               TGATCAGTAT                          451                                                                               CCctTgGGAC                                                                               GAAGCTT                                                           HPV40 (SEQ ID NO: 286)                                                         1  CAAAAGGCCC                                                                               AGGGCCATAA                                                                               CAATGGCATA                                                                               TGTTTTGGCA                                                                               ATCAGTTATT                          51 TGTTACAGTT                                                                               GTAGACACCA                                                                               CTCGTAGCAC                                                                               TAATTTGACC                                                                               TTATGTGCTG                          101                                                                               CCACACAGGG                                                                               CCCCACACCA                                                                               GGCCCATATA                                                                               ATAACAGTAA                                                                               TTTCAAGGAA                          151                                                                               TATTTGCGTC                                                                               AGGGGGAGGA                                                                               GTTTGATTTG                                                                               CAGTTTATTT                                                                               TTCAGTTATG                          201                                                                               TGTAATTACC                                                                               TTAAATGCAG                                                                               AGGTTATGAC                                                                               ATATATTCAT                                                                               GCAATGGATC                          251                                                                               CTACGTTGTT                                                                               GGAGGATTGG                                                                               AACTTTAAAA                                                                               TTGCTCCTCC                                                                               AGCCTCTGCA                          301                                                                               TCCTTAGAGG                                                                               ATACATATAG                                                                               GTTCCTTACC                                                                               AACAAGGCTA                                                                               TTGCCTGTCA                          351                                                                               GCGCGATGCC                                                                               GCCCCCAAGG                                                                               TACGGGAGGA                                                                               TCCATATAAA                                                                               AAATATAAAT                          401                                                                               TTTGGGATGT                                                                               CAATTTAACA                                                                               GAAAGATTTT                                                                               CTTCCCAATT                                                                               AGATCAATTT                          451                                                                               CCATTAGGAC                                                                               GTAAGTT                                                           HPV42 (SEQ ID NO: 287)                                                         1  GAGCTCGCAC                                                                               AGGGTCATAA                                                                               TAATGGTATA                                                                               TGTTGGGGAA                                                                               ATCAGCTATT                          51 TTTAACTGTG                                                                               GTTGATACTA                                                                               CCCGTAGTAC                                                                               TAACATGACT                                                                               TTGTGTGCCA                          101                                                                               CTGCAACATC                                                                               TGGTGATACA                                                                               TATACAGCTG                                                                               CTAATTTTAA                                                                               GGAATATTTA                          151                                                                               AGACATGCTG                                                                               AAGAATATGA                                                                               TGTGCAATTT                                                                               ATATTTCAAT                                                                               TIGTGTAAAAT                         201                                                                               AACATTAACT                                                                               GTTGAAGTTA                                                                               TGTCATATAT                                                                               ACACAATATG                                                                               AATCCTAACA                          251                                                                               TATTAGAGGA                                                                               GTGGAATGTT                                                                               GGTGTTGCAC                                                                               CACCACCTTC                                                                               AGGAACTTTA                          301                                                                               GAAGATAGTT                                                                               ATAGGTATGT                                                                               ACAATCAGAA                                                                               GCTATTCGCT                                                                               GTCAGGCTAA                          351                                                                               GGTAACAACG                                                                               CCAGAAAAAA                                                                               AGGATCCTTA                                                                               TTCAGACTTT                                                                               TCCTTTTGGG                          401                                                                               AGGTAAATTT                                                                               ATCTGAAAAG                                                                               TTTTCTACTG                                                                               ATTTAGATCA                                                                               GTATCCTCTG                          451                                                                               GGACGAAGCT                                                                               T                                                                 HPV45 (SEQ ID NO: 288)                                                         1  GAGCTCGCAC                                                                               AGGGTCATAA                                                                               CAATGGTATT                                                                               TGTTGGCATA                                                                               ATCAGTTGTT                          51 TGTTGCTGTA                                                                               GTGGACACTA                                                                               CCCGCAGTAC                                                                               TAATTTAACA                                                                               TTATGTGCCT                          101                                                                               CTACACAAAA                                                                               TCCTGTGCCA                                                                               AGTACATATG                                                                               ACCCTACTAA                                                                               GTTTAAGCAG                          151                                                                               TATAGTAGAC                                                                               ATGTGGAGGA                                                                               ATATGATTTA                                                                               CAGTTTATTT                                                                               TTCAGTTGTG                          201                                                                               CACTATTACT                                                                               TTAACTGCAG                                                                               AGGTTATGTC                                                                               ATATATCCAT                                                                               AGTATGAATA                          251                                                                               GTAGTATATT                                                                               AGAAAATTGG                                                                               AATTTTGGTG                                                                               TCCCTCCACC                                                                               ACCTACTACA                          301                                                                               AGTTTGGTGG                                                                               ATACATATCG                                                                               TTTTGTGCAA                                                                               TCAGTTGCTG                                                                               TTACCTGTCA                          351                                                                               AAAGGATACT                                                                               ACACCTCCAG                                                                               AAAAGCAGGA                                                                               TCCATATGAT                                                                               AAA7rAAAGT                          401                                                                               TTTGGACTGT                                                                               TGACCTAAAG                                                                               GAAAAATTTT                                                                               CCTCCGATTT                                                                               GAATCAGTAT                          451                                                                               CCCTTGGGAC                                                                               GAAGCTT                                                           HPV51 (SEQ ID NO: 289)                                                         1  TCCACCGTGC                                                                               GCAGGGTCAC                                                                               AATAATGGCA                                                                               TTTGCTGGAA                                                                               CAATCAGCTT                          51 TTTATTACCT                                                                               GTGTTGATAC                                                                               TACCAGAAGT                                                                               ACAAATTTAA                                                                               CTATTAGCAC                          101                                                                               TGCCACTGCT                                                                               GCGGTTTCCC                                                                               CAACATTTAC                                                                               TCCAAGTAAC                                                                               TTTAAGCAAT                          151                                                                               ATATTAGGCA                                                                               TGGGGAAGAG                                                                               TATGAATTGC                                                                               AATTTATTTT                                                                               TCAATTATGT                          201                                                                               AAAATTACTT                                                                               TAACTACAGA                                                                               GGTAATGGCT                                                                               TATTTACACA                                                                               CAATGGATCC                          251                                                                               TACCATTCTT                                                                               GAACAGTGGA                                                                               ATTTTGGATT                                                                               AACATTACCT                                                                               CCGTCTGCTA                          301                                                                               GTTTGGAGGA                                                                               TGCATATAGG                                                                               TTTGTTAGAA                                                                               ATGCAGCTAC                                                                               TAGCTGTCAA                          351                                                                               AAGGACACCC                                                                               CTCCACAGGC                                                                               TAAGCCAGAT                                                                               CCTTTGGCCA                                                                               AATATAAATT                          401                                                                               TTGGGATGTT                                                                               GATTTAAAGG                                                                               AACGATTTTC                                                                               TTTAGATTTA                                                                               GACCAATTT                           HPV52 (SEQ ID NO: 290)                                                         1  GAGCTCGCCC                                                                               AGGGTCATAA                                                                               TAATGGCATA                                                                               TGTTGGGGCA                                                                               ATCAGTTGTT                          51 TGTCACAGTT                                                                               GTGGATACCA                                                                               CTCGTAGCAC                                                                               TAACATGACT                                                                               TTATGTGCTG                          101                                                                               AGGTTAGAAA                                                                               GGAAAGCACA                                                                               TATAAAAATG                                                                               AAAATTTTAA                                                                               GGAATACCTT                          151                                                                               CGTCATGGCG                                                                               AGGAATTTGA                                                                               TTTACAATTT                                                                               ATTTTTCAAT                                                                               TGTGCAAAAT                          201                                                                               TACATTAACA                                                                               GCTGATGTTA                                                                               TGACATACAT                                                                               TCATAAGATG                                                                               GATGCCACTA                          251                                                                               TTTTAGAGGA                                                                               CTGGCAATTT                                                                               GGCCTTACCC                                                                               CACCACCGTC                                                                               TGCATCTTTG                          301                                                                               GAGGACACAT                                                                               ACAGATTTGT                                                                               CACTTCTACT                                                                               GCTATAACTT                                                                               GTCAAAAAAA                          351                                                                               CACACCACCT                                                                               AAAGGAAAGG                                                                               AAGATCCTTT                                                                               AAAGGACTAT                                                                               ATGTTTTGGG                          401                                                                               AGGTGGATTT                                                                               AAAAGAAAAG                                                                               TTTTCTGCAG                                                                               ATTTAAATCA                                                                               GTATCCTTTT                          451                                                                               GGACGAAGCT                                                                               T                                                                 HPV53 (SEQ ID NO: 291)                                                         1  GAGCTCGCCC                                                                               AGGGTCATAA                                                                               TAATGGCATC                                                                               TGTTGGAACA                                                                               ATCAGTTATT                          51 TGTAACTGTT                                                                               GTGGATACCA                                                                               CCAGGAATAC                                                                               AAACATGACT                                                                               CTTTCCGCAA                          101                                                                               CCACACAGTC                                                                               TATGTCTACA                                                                               TATAATTCAA                                                                               AGCAAATTAA                                                                               ACAGTATGTT                          151                                                                               AGACATGCAG                                                                               AGGAATATGA                                                                               ATTACAATTT                                                                               GTGTTTCAAC                                                                               TATGTAAAAT                          201                                                                               ATCCCTGTCT                                                                               GCTGAGGTTA                                                                               TGGCCTATTT                                                                               ACATACTATG                                                                               AATTCTACCT                          251                                                                               TACTGGAAGA                                                                               CTGGAATACA                                                                               GGTTTGTCGC                                                                               CTCCTGTTGC                                                                               CACTAGCTTA                          301                                                                               GAGGACAAAT                                                                               ACAGATATGT                                                                               GAAAAGTGCA                                                                               GCTATAACCT                                                                               GTCAAAAGGA                          351                                                                               TCAGCCCCCT                                                                               CCTGAAAAGC                                                                               AGGACCCACT                                                                               ATCTAAATAT                                                                               AAATTTTGGG                          401                                                                               AGGTCAATTT                                                                               GCAAAACAGT                                                                               TTTTCTGCTG                                                                               ATTTGGATCA                                                                               GTATCCCCTG                          451                                                                               GGACGAAGCT                                                                               T                                                                 HPV54 (SEQ ID NO: 292)                                                         1  GAGCTCGCAC                                                                               AGGGTCATAA                                                                               TAATGGTATT                                                                               TGTTGGGGCA                                                                               ATCAATTGTT                          51 TTTAACAGTT                                                                               GTAGATACCA                                                                               CCCGTAGTAC                                                                               TAACCTAACA                                                                               TTGTGTGCTA                          101                                                                               CAGCATCCAC                                                                               GCAGGATAGC                                                                               TTTAATAATT                                                                               CTGACTTTAG                                                                               GGAGTATATT                          151                                                                               AGACATGTGG                                                                               AGGAATATGA                                                                               TTTACAGTTT                                                                               ACATTTCAGT                                                                               TATGTACCAT                          201                                                                               AGCCCTTACA                                                                               GCAGATGTTA                                                                               TGGCCTATAT                                                                               TCATGGAATG                                                                               AATCCCACTA                          251                                                                               TTCTAGAGGA                                                                               CTGGAACTTT                                                                               GGTATAACCC                                                                               CCCCAGCTAC                                                                               AAGTAGTTTG                          301                                                                               GAGGACACAT                                                                               ATAGGTTTGT                                                                               ACAGTCACAG                                                                               GCCATTGCAT                                                                               CTCAAAAGAA                          351                                                                               TAATGCCCCT                                                                               GCAAAGGAAA                                                                               AGGAGGATCC                                                                               TTACAGTAAA                                                                               TTTACTTTTT                          401                                                                               GGACTGTTGA                                                                               CCTTAAGGAA                                                                               CGATTTTCAT                                                                               CTGACCTTGA                                                                               TCAGTATCCC                          451                                                                               CTTGGACGAA                                                                               GCTT                                                              HPV55 (SEQ ID NO: 293)                                                         1  GCGCAGGGCC                                                                               ACAATAATGG                                                                               TATTTGTTGG                                                                               GGGAATCAGT                                                                               TATTTGTTAC                          51 TGTTGTAGAT                                                                               ACTACACGTA                                                                               GTACAAACAT                                                                               GACAATATGT                                                                               GCTGCTACAA                          101                                                                               CTCAGTCTCC                                                                               ATCTACAACA                                                                               TATAATAGTA                                                                               CAGAATATAA                                                                               ACAATACATG                          151                                                                               CGACATGTTG                                                                               AGGAGTTTGA                                                                               CTTACAGTTT                                                                               ATGTTTCAAT                                                                               TATGTAGTAT                          201                                                                               TACCTTAACT                                                                               GCTGAGGTAA                                                                               TGGCCTATTT                                                                               ACATACCATG                                                                               AATCCTGGTA                          251                                                                               TTTTGGAACA                                                                               GTGGAACTTT                                                                               GGGTTGTCGC                                                                               CACCCCCAAA                                                                               TGGTACCTTA                          301                                                                               GAAGACAAAT                                                                               ACAGATATGT                                                                               GCAGTCACAG                                                                               GCCATTACAT                                                                               GTCAAAAGCC                          351                                                                               TCCCCCTGAA                                                                               AAGGCAAAGC                                                                               AGGACCCCTA                                                                               TGCAAAATTA                                                                               AGTTTTTGGG                          401                                                                               AGGTAGATCT                                                                               CAGAGAAAAG                                                                               TTTTCTAGTG                                                                               AGTTAGATCA                                                                               ATATCCCCTT                          451                                                                               GGTAG                                                                       HPV56 (SEQ ID NO: 294)                                                         1  GAGCTCGCAC                                                                               AGGGACATAA                                                                               TAATGGCATT                                                                               TGCTGGGGTA                                                                               ATCAATTATT                          51 TGTGACTGTA                                                                               GTAGATACTA                                                                               CTAGAAGTAC                                                                               TAACATGACT                                                                               ATTAGTACTG                          101                                                                               CTACAGAACA                                                                               GTTAAGTAAA                                                                               TATGATGCAC                                                                               GAAAAATTAA                                                                               TCAGTACCTT                          151                                                                               AGACATGTGG                                                                               AGGAATATGA                                                                               ATTACAATTT                                                                               GTTTTTCAAT                                                                               TATGCAAAAT                          201                                                                               TACTTTGTCT                                                                               GCAGAGGTTA                                                                               TGGCATATTT                                                                               ACATAATATG                                                                               AATGCTAACC                          251                                                                               TACTGGAGGA                                                                               CTGGAATATT                                                                               GGGTTATCCC                                                                               CGCCAGTGGC                                                                               CACCAGCCTA                          301                                                                               GAAGATAAAT                                                                               ATAGATATGT                                                                               TAGAAGCACA                                                                               GCTATAACAT                                                                               GTCAACGGGA                          351                                                                               ACAGCCACCA                                                                               ACAGAAAAAC                                                                               AGGACCCATT                                                                               AGCTAAATAT                                                                               AAATTTTGGG                          401                                                                               ATGTTAACTT                                                                               ACAGGACAGT                                                                               TTTTCTACAG                                                                               ACCTGGATCA                                                                               GTATCCCTTG                          451                                                                               GGACGAAGCT                                                                               T                                                                 HPV57 (SEQ ID NO: 295)                                                         1  GCCCAGGGAC                                                                               ATAACAATGG                                                                               CATGTGCTGG                                                                               GGCAATCGGA                                                                               TCTTCCTAAC                          51 AGTGGTGGAC                                                                               ACCACGCGCA                                                                               GCACAAATGT                                                                               CTCTTTGTGT                                                                               GCCACTGTAA                          101                                                                               CCACAGAAAC                                                                               TAATTATAAA                                                                               GCCTCCAATT                                                                               ATAAGGAATA                                                                               CCTTAGGCAT                          151                                                                               ATGGAGGAAT                                                                               ATGATTTGCA                                                                               GTTCATTTTT                                                                               CAACTGTGCA                                                                               AAATAACACT                          201                                                                               CACCCCCGAG                                                                               ATAATGGCAT                                                                               ACATACATAA                                                                               CATGGATGCG                                                                               CGGTTGCTAG                          251                                                                               AGGACTGGAA                                                                               CTTTGGTGTC                                                                               CCCCCACCCC                                                                               CGTCCGCCAG                                                                               CCTGCAGGAC                          301                                                                               ACCTACAGGT                                                                               ATTTGCAATC                                                                               CCAAGCGATA                                                                               ACATGTCAGA                                                                               AGCCCACACC                          351                                                                               CCCTAAGACC                                                                               CCTACTGATC                                                                               CCTATGCAAC                                                                               CATGACATTC                                                                               TGGGATGTGG                          401                                                                               ATCTCAGTGA                                                                               AAGTTTTTCC                                                                               ATGGATCTGG                                                                               ACCAATTCCC                                                                               CCTGGGACG                           HPV59 (SEQ ID NO: 296)                                                         1  CACAAGGCTC                                                                               AGGGTTTAAA                                                                               CAATGGTATA                                                                               TGTTGGCACA                                                                               ATCAATTGTT                          51 TTTAACAGTT                                                                               GTAGATACTA                                                                               CTCGCAGCAC                                                                               CAATCTTTCT                                                                               GTGTGTGCTC                          101                                                                               TACTACTCTC                                                                               TATTCCTAAT                                                                               GTATACACAC                                                                               CTACCAGTTT                                                                               TAAAGAATAT                          151                                                                               GCCAGACATG                                                                               TGGAGGAATT                                                                               TGATTTGCAG                                                                               TTTATATTTC                                                                               AACTGTGTAA                          201                                                                               AATAACATTA                                                                               ACTACAGAGG                                                                               TAATGTCATA                                                                               CATTCATAAT                                                                               ATGAATACCA                          251                                                                               CTATTTTGGA                                                                               GGATTGGAAT                                                                               TTTGGTGTTA                                                                               CACCACCTCC                                                                               TACTGCTAGT                          301                                                                               TTAGTTGACA                                                                               CATACCGTTT                                                                               TGTTCAATCT                                                                               GCTGCTGTAA                                                                               CTTGTCAAAA                          351                                                                               GGACACCGCA                                                                               CCGCCAGTTA                                                                               AACAGGACCC                                                                               TTATGACAAA                                                                               CTAAAGTTTT                          401                                                                               GGCCTGTAGA                                                                               TCTTAAGGAA                                                                               AGGTTTTCTG                                                                               CAGATCTTGA                                                                               TCAGTTTCCT                          451                                                                               TTGGGACGTA                                                                               AATT                                                              __________________________________________________________________________

Isolate 36A is an HPV59 variant, and isolate 36B is an HPV42 variant. Isolate 238B corresponds to the HPV31 type described in the literature. A cervical carcinoma isolate, C14, is a variant of HPV45. Isolate B6062 is an HPV26, isolate D3173 is an HPV53 variant, and isolate B8988 is an HPV68.

Those skilled in the art will recognize that with the above sequence information, primers and probes for amplifying and detecting these new HPV isolates can be obtained. In addition, these sequences enable one to isolate the entire virus from samples containing the virus. The discovery of these new HPV isolates led to the creation of additional L1 consensus oligonucleotide probes for use in conjunction with FS10 (Seq ID No. 21), MY18 (Seq ID No. 106), and MY19 (Seq ID No. 271). These L1 consensus probes are depicted below under the FS10 (Seq ID No. 21) probe sequence to demonstrate the similarity to the FS10 (Seq ID No. 21) sequence. L1 consensus probe WD147 (Seq ID No. 27) will hybridize to HPV45 DNA. MY46 (Seq ID No. 28) is a combination of FS10 (Seq ID No. 21) and MY19 (Seq ID No. 271). In one embodiment, a consensus L1 probe can be an equimolar mixture of MY18 (Seq ID No. 106), MY46 (Seq ID No. 28), MY57 (Seq ID No. 26), and WD147 (Seq ID No. 27).

    __________________________________________________________________________     Seg ID                                                                         No.        Sequence                                                            __________________________________________________________________________     FS10 21    5'                                                                               C T G T G G T A G A T A C C A C A C G C A G T A C                 MY66 22      --                                                                               A --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --      T                                                                              --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               C -- --               MY55 23      --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --      C                                                                              --                                                                             --                                                                             T --                                                                               --                                                                               --                                                                               -- --               MY39 24      --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               G --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --      C                                                                              A                                                                              --                                                                             A --                                                                               --                                                                               C -- --               MY56 25      --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --      T                                                                              A                                                                              --                                                                             A --                                                                               --                                                                               C -- --               MY57 26      --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --      --                                                                             --                                                                             --                                                                             T --                                                                               --                                                                               --                                                                               -- --               WD147                                                                               27      --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               G --                                                                               --                                                                               C --                                                                               --                                                                               T --                                                                               --      C                                                                              --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                                                                               -- --               MY46 28      --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --      W                                                                              --                                                                             --                                                                             --                                                                               --                                                                               --                                                                               --                                                                               -- --               __________________________________________________________________________

Example 4, below, describes the creation of an alternate long genetic probe with enhanced detection capabilities. In particular, the long generic probe described in Example 4 has the ability to detect HPV51.

The present invention provides a number of probes for typing amplified DNA produced from L1 consensus primers. While most probes for typing HPV hybridize to known HPV types, others specifically detect previously uncharacterized HPV types and hybridize to novel HPVs identified in clinical samples as a result of use of the present methods. These type-specific probes are depicted below in Tables 5 and 5a.

                                      TABLE 5                                      __________________________________________________________________________     HPV Typing Probes For Use with L1 Consensus Primers                                 Sequence                            Genome  5' Biotinylated               Probe                                                                               ID No.                                                                               Specificity                                                                          Sense                                                                              Seguence            Position                                                                               Versions                      __________________________________________________________________________     MY12 142   HPV6  +   CATCCGTAACTACATCTTCCA                                                                              6813    MY134                         MY62 143   HPV6  +   CTCCTGAAAAGGAAAAGCCA                                                                               7068                                  MY63 144   HPV6  -   TGGCTTTTCCTTTTCAGGAG                                                                               7068    MY135                         MY125                                                                               145   HPV6/ +   ACAATGAATCCYTCTGTTTTGG                                                                             6950/6935                                                                              MY138                                    HPV11                                                               MY126                                                                               146   HPV6/ +   ATCGCCTCCMCCAAATG   6991/6976                                        HPV11                                                               MY13 147   HPV11 +   TCTGTGTCTAAATCTGCTACA                                                                              6800    MY136                         MY61 148   HPV11 +   CACACCTGAAAAAGAAAAACAG                                                                             7051                                  MY65 149   HPV11 -   CTGTTTTTCTTTTTCAGGTGTG                                                                             7051    MY137                         WD150                                                                               150   HPV11 +   CAGAAACCCACACCTGAAAAAGA                                                                            7059                                  WD151                                                                               151   HPV11 +   AGAAACCCACACCTGAAAAAGAA                                                                            7058                                  MY14 152   HPV16 +   CATACACCTCCAGCACCTAA                                                                               6926    MY14                          MY58 153   HPV16 +   TTGTAACCCAGGCAATTGCT                                                                               6895                                  MY71 154   HPV16 +   ACATACACCTCCAGCACCTA                                                                               6923                                  MY72 155   HPV16 +   CATACACCTCCAGCACCTA 6924                                  MY95 156   HPV16 -   GATATGGCAGCACATAATGAC                                                                              6685    MY139                         MY96 157   HPV16 -   AGTTTCTGAAGTAGATATGGCA                                                                             6674                                  MY97 158   HPV16 -   CTGAAGTAGATATGGCAGCAC                                                                              6670                                  MY133                                                                               159   HPV16 +   GTAACATCCCAGGCAATTG 6897    MY140                         WD152                                                                               160   HPV16 +   TTTGTAACCCAGGCAATTGCT                                                                              6894                                  WD153                                                                               161   HPV16 +   GTTTGTAACCCAGGCAATTGCT                                                                             6893                                  MY60 162   HPV18 +   CAGTCTCCTGTACCTGGG  6657                                  MY73 163   HPV18 +   GATGCTGCACCGGCTGAA  6906                                  MY107                                                                               164   HPV18 -   GCCCAGGTACAGGAGAC   6659                                  MY130                                                                               165   HPV18 +   GGGCAATATGATGCTACCAAT                                                                              6672    MY142                         MY131                                                                               166   HPV18 +   GTACCTGGGCAATATGATG 6666                                  MY132                                                                               167   HPV18 +   TCTCCTGTACCTGGGCAA  6660                                  WD74 168   HPV18 +   GGATGCTGCACCGGCTGA  6905    MY141                         WD75 169   HPV18 -   TCAGCCGGTGCAGCATCC  6905                                  WD126                                                                               170   HPV31 +   CCAAAAGCCCAAGGAAGATC                                                                               6851                                  WD127                                                                               171   HPV31 +   CAAAAGCCCAAGGAAGATC 6852                                  WD128                                                                               172   HPV31 +   TTGCAAACAGTGATACTACATT                                                                             6597    MY143                         MY109                                                                               173   HPV31 -   GAGGGAGGTGTGGTCAAT  6769                                  MY110                                                                               174   HPV31 -   AAGAACCTGAGGGAGGT   6778                                  MY92 175   HPV31/                                                                               +   CCAAAAGCCYAAGGAAGATC                                                                               6853    MY144                                    HPV31B                                                              MY127                                                                               176   HPV31/                                                                               +   ACCACACCTCCCTCAG    6773                                             HPV31B                                                              MY128                                                                               177   HPV31/                                                                               +   ACAGGCCATTACATGTCAA 6823                                             HPV31B                                                              MY16 178   HPV33 +   CACACAAGTAACTAGTGACAG                                                                              6628    MY145                         MY59 179   HPV33 +   AAAAACAGTACCTCCAAAGGA                                                                              6877                                  MY64 180   HPV33 -   TCCTTTGGAGGTACTGTTTTT                                                                              6877    MY146                         MY115                                                                               181   HPV35 +   CTGCTGTGTCTTCTAGTGACAG                                    MY116                                                                               182   HPV35 +   TGCACCAAAACCTAAAGATG                                      MY117                                                                               183   HPV35 -   ATCATCTTTAGGTTTTGGTGC                                     MY89 184   HPV39 +   TAGAGTCTTCCATACCTTCTAC      MY147                         MY90 185   HPV39 +   CTGTAGCTCCTCCACCATCT        MY148                         MY91 186   HPV39 +   AGACACTTACAGATACCTACAG                                    MY118                                                                               187   HPV40 +   CACACCAGGCCCATATAAT                                       MY119                                                                               188   HPV40 +   CCAAGGTACGGGAGGATC                                        MY120                                                                               189   HPV40 -   GATCCTCCCGTACCTTG                                         MY121                                                                               190   HPV42 +   CACTGCAACATCTGGTGAT                                       MY122                                                                               191   HPV42 -   TCACCAGATGTTGCAGTG                                        MY33 192   HPV42 -   GGCGTTGYTTACCTTAGCC                                       MY34 193   HPV42 +   GGCTAAGGTAACAACGCC                                        MY68 194   HPV45 +   GGATACTACACCTCCAG                                         MY69 195   HPV45 +   ATACTACACCTCCAGAAAAGC       MY149                         MY70 196   HPV45 +   TAGTGGACACTACCCGCAG                                       MY98 197   HPV45 -   GCACAGGATTTTGTGTAGAGG                                     MY99 198   HPV45 -   TGTATTTGGCACAGGATTTTG                                     MY100                                                                               199   HPV45 -   CAGGATTTTGTGTAGAGGCA                                      MY108                                                                               200   HPV45 +   CAAATCCTGTGCCAGGTAC                                       MY129                                                                               201   HPV45 -   GCACAGGATTTTGTGTAGAG        MY150                         MY87 202   HPV51 +   TATTAGCACTGCCACTGCTG                                      MY88 203   HPV51 +   CCCAACATTTACTCCAAGTAAC                                    MY80 204   HPV52 +   CTGAGGTTAGAAAGGAAAGCA                                     MY81 205   HPV52 +   CACTTCTACTGCTATAACTTGT                                    MY82 206   HPV52 +   ACACACCACCTAAAGGAAAGG                                     MY101                                                                               207   HPV53 +   CGCAACCACACAGTCTATGT                                      MY102                                                                               208   HPV53 +   TTCTACCTTACTGGAAGACTGG                                    MY103                                                                               209   HPV53 +   GGAGGTCAATTTGCAAAAC                                       MY111                                                                               210   HPV54 -   TGCAGGGGCATTATTCTTT                                       MY112                                                                               211   HPV54 +   TACAGCATCCACGCAG                                          MY113                                                                               212   HPV54 +   CACGCAGGATAGCTT                                           MY114                                                                               213   HPV54 +   CCACGCAGGATAGCTT                                          MY151                                                                               214   HPV55 +   GTGCTGCTACAACTCAGTCT                                      MY152                                                                               215   HPV55 +   GCTACAACTCAGTCTCCATC                                      MY153                                                                               216   HPV55 -   TGCCTTTTCAGGGGGAG                                         MY154                                                                               217   HPV57 +   AATGTCTCTTTGTGTGCCAC                                      MY155                                                                               218   HPV57 +   GTGTGCCACTGTAACCACA                                       MY156                                                                               219   HPV57 -   GGATCAGTAGGGGTCTTAGG                                      MY93 220   HPV58 +   GCACTGAAGTAACTAAGGAAGG                                    MY94 221   HPV58 +   AGCACCCCCTAAAGAAAAGGA                                     MY123                                                                               222   HPV59 +   GCCAGTTAAACAGGACCC                                        MY124                                                                               223   HPV59 -   CATAAGGGTCCTGTTTAACTG                                     MY83 224   PAP88 +   ATTAATGCAGCTAAAAGCACATT                                   MY84 225   PAP88 +   GATGCCCGTGAAATCAATCAA                                     MY86 226   PAP155                                                                               +   TACTTGCAGTCTCGCGCCA                                       MY85 227   PAP155                                                                               +   CCAACACCGAATCAGAATATAAA                                   MY104                                                                               228   PAP238A                                                                              +   GTAGGTACACAGGCTAGTAGCTC                                   MY105                                                                               229   PAP238A                                                                              +   GCTCTACTACAACGTATGCCA                                     MY106                                                                               230   PAP238A                                                                              +   AGTTGCCAACGTCCTCAAC                                       __________________________________________________________________________

                                      TABLE 5A                                     __________________________________________________________________________     Additional HPV Type Probes for Use With L1 Consensus Primers                   Probe Seg. ID No.                                                                           HPV Type                                                                              Seguence                                                   __________________________________________________________________________     MYB186                                                                               29     HPV26  GCTGACAGGTAGTAGCAGAGTT                                     MYB187                                                                               30     HPV26  GCCATAACATCTGTTGTAAGTG                                     MYB188                                                                               31     HPV26  GAGTGGATGCAGATGCTG                                         MYB189                                                                               32     HPV26  CTAATGGTAAGGTTAGTACTGCG                                    MYB202                                                                               33     HPV26  CAGCATCTGCATCCACTC                                         MYB168                                                                               34     HPV35  ACCCAGTGCACCAAAACC                                         MYB169                                                                               35     HPV35  CCAAAACCTAAAGATGATCCAT                                     MYB174                                                                               36     HPV40  CACCAGGCCCATATAATAACAG                                     MYB175                                                                               37     HPV40  TGTCAGCGCGATGCC                                            MYB182                                                                               38     HPV53  GCAACCACACAGTCTATGTC                                       MYB159                                                                               39     HPV53  GACTCTTTCCGCAACCACAC                                       MYB160                                                                               40     HPV54  CAGCATCCACGCAGGATAG                                        MYB161                                                                               41     HPV54  GAATAATGCCCCTGCAAAG                                        MYB170                                                                               42     HPV55  CAAATACAGATATGTGCAGT                                       MYB151                                                                               43     HPV55  GTGCTGCTACAACTCAGTCT                                       MYB171                                                                               44     HPV55  CCCTGAAAAGGCAAAGCAG                                        MYB196                                                                               45     HPV56  GCTAACCTACTGGAGGACTGG                                      MYB197                                                                               46     HPV56  GCACAGCTATAACATGTCAACG                                     MYB198                                                                               47     HPV56  CCTCCACATGTCTAAGGTACTG                                     MYB199                                                                               48     HPV56  CAGTTAAGTAAATATGATGCACG                                    MYB172                                                                               49     HPV59  ACACCSCACCGCCAGTT                                          MYB173                                                                               50     HPV59  TTAAACAGGACCCTTATGACA                                      MYB162                                                                               51     HPV59  CCTAATGWATACACACCTACCAG                                    MYB176                                                                               52     HPV40  CCCAAGGTACGGAGGATCC                                        MYB191                                                                               66     HPV68  CATACCGCTATCTGCAATCAG                                      MYB192                                                                               53     HPV68  GATGGCTTAAACTTTTGGAATG                                     MYB193                                                                               54     HPV68  CAATCAGCAGCAATTACATG                                       MYB194                                                                               67     HPV68  CTACTACTGAATCAGCTGTACC                                     MYB195                                                                               55     HPV68  CATGTAATTGCTGCTGATTG                                       MYB177                                                                               56     PAP88  TCCCCACCAGTTGCAACTAG                                       MYB178                                                                               57     PAP88  CATGTCAGAGGGAACAGCC                                        MYBI63                                                                               58     PAP155 GTTGTGCCCCCTCCCTCCA                                        MYB179                                                                               59     PAP251 GACATTATGCACTGAAGTAACTAAG                                  MYB166                                                                               60     PAP291 GGCTAATGAATACACAGCCTC                                      MYB167                                                                               61     PAP291 TCCTTCCACCAGCCTTGAT                                        MYB180                                                                               62     PAP291 CGCTATCTGCAGTCCCGTGC                                       MYB181                                                                               63     PAP291 CTGCAGTCCCGTGCTATTACC                                      MYB164                                                                               64     W13B   CTCAATCTGTTGCACAAACA                                       MYB165                                                                               65     W13B   TAACCTTGCCCCCCTCAG                                         __________________________________________________________________________

In another aspect of the invention, improved primers are provided for amplification of HPV-51. Consensus L1 primers MY09 (Seq ID No. 269) and MY11 (Seq ID No. 267) are suitable for amplifying the L1 region of any HPV type present in a sample. However, MY09 (Seq ID No. 269) preferentially binds to HPV-51 at an internal site approximately 200 base pairs upstream of the expected MY09 (Seq ID No. 269) binding site. This can cause less efficient amplification of the HPV-51 450 bp product compared to other HPVs, and thus, lead to a false negative result. To produce a full length (450 bp) PCR product for HPV-51 with efficiency comparable to other HPV targets, a primer specific for HPV-51 is desirable in combination with the consensus primers MY09 (Seq ID No. 269) and MY 11 (Seq ID No. 267). For example, CEG05 (Seq. ID No. 94), HMB01 (Seq ID No. 95), HMB02 (Seq ID No. 96), HMB03 (Seq ID No. 97), and HMB04 (Seq ID No. 98) are oligonucleotides that are analogous to MY09 (Seq ID No. 269) and promote the amplification of the HPV-51 450 bp L1 PCR product. These sequences are provided below.

    ______________________________________                                         CEG05   Seq. ID No. 94                                                                             CGACCCAATGCAAATTGGTC                                       HMB01   Seq. ID No. 95                                                                             GCGACCCAATGCAAATTGGT                                       HMB02   Seq. ID No. 96                                                                             TGCGACCCAATGCAAATTGG                                       HMB03   Seq. ID No. 97                                                                             CTTGCGACCCAATGCAAATT                                       HMB04   Seq. ID No. 98                                                                             GACCCAATGCAAATTGGTCT                                       ______________________________________                                    

By adding any of the above primers to MY09/MY11 (Seq ID No. 269/Seq ID No. 267) the sensitivity of the L1 PCR system is substantially increased for HPV-51, and false negatives are avoided.

Following amplification of HPV-51 DNA, the PCR product can be detected by a type-specific probe or by use of labeled primers to generate a detectable nested product. For example, primers CEG03 (Seq ID No. 99) and CEG04 (Seq ID No. 100) are internal to the L1 consensus primers HMB01/MY11 (Seq ID No. 95/Seq ID No. 267) and generate a detectable HPV-51 product 412 bp in size.

    ______________________________________                                         CEG03   Seq ID No.                                                                               CATTTGCTGGAACAATCAG                                                  99                                                                     CEG04   Seq ID No.                                                                               TAAATCTAAAGAAAATCGTTCCT                                              100                                                                    ______________________________________                                    

E6 Region

The present invention also provides consensus primers and HPV typing probes specific for the E6 region of genital HPVs. These probes are particularly preferred, because in some cancers, the HPV genome is partially deleted or rearranged such that only E6- and E7-related sequences are present. The E6 consensus primer pairs of the invention comprise primer pairs in which one primer is complementary to sequences near the border of the URR and E6 regions and the other primer is complementary to sequences in either the E7 region near the E6-E7 border (the E6 and E7 open reading frames overlap) or in the E6 region. These E6 consensus primers are depicted below in Tables 6a, 6b, and 6c. The use of E6 region as a second site for detection and typing may allow detection of integrated HPVs. The smaller E6 PCR products also increase the likelihood of detecting HPV sequences in archival tissues where DNA may be too fragmented to serve as a template for long PCR products.

E6 consensus primers, consensus probes, and type-specific probes are suitable for detecting and typing HPV nucleic acids, either alone or in conjunction with L1 primers and probes. In one embodiment of the invention, the E6 gene was chosen as a site for a second consensus primer set and type specific probes. While it is not an essential aspect of the present invention, the use of two sites allows rapid confirmation of typing results, thereby increasing the confidence level of the data. The use of a second site also circumvents the prospect of false negativity as a consequence of sequence variation in one of the primer binding sites.

                                      TABLE 6a                                     __________________________________________________________________________     E6 Consensus Primers                                                           URR/E6 Consensus Positive Strand Primers                                       __________________________________________________________________________     WD73                                                                               (Seq ID No. 123)                                                                        5'                                                                               C G G T T S A   A C C G A A A A C G G                           WD72                                                                               (Seq ID No. 124)                                                                        5'                                                                               C G G T C G G G A C C G A A A A      C                                                                       G      G                          WD76                                                                               (Seq ID No. 125)                                                                        5'                                                                               C G G T T S A   A C C G A A A M      C                                                                       G      G                          WD77                                                                               (Seq ID No. 126)                                                                        5'                                                                               C G G T T C A   A C C G A A A M      C                                                                       G      G                          HPV6                                                                               43       5'                                                                               C G G T T C A   A C C G A A A A      C                                                                       G      G                          HPV11                                                                              43         --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --  --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                         HPV16                                                                              43         --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               G --  --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               C      --                                                                      --     --                         HPV18                                                                              43         --                                                                               --                                                                               --                                                                               --                                                                               C G G G --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                         HPV31                                                                              45         G T --                                                                               G --                                                                               G --  --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                         HPV33                                                                              65         --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --  --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                         __________________________________________________________________________

The URR/E6 positive strand primers are used as mixtures: WD72 (Seq ID No. 124) and WD73 (Seq ID No. 123); WD72 (Seq ID No. 124) and WD76 (Seq ID No. 125); and WD72 (Seq ID No. 124) and WD77 (Seq ID No. 126).

                                      TABLE 6b                                     __________________________________________________________________________     E7 Consensus Negative Strand Primer                                            __________________________________________________________________________     WD70                                                                               (Seq ID No. 127)                                                                        G C R C A G A T G G G R C A C A C                                 WD71                                                                               (Seq ID No. 128)                                                                        G C A C A C C A C G G A C A C A C                                 HPV06                                                                              813      G C G C A G A T G G G A C A C A C                                 HPV11                                                                              813      --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                HPV16                                                                              845      --                                                                               A A --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               G --                                                                               --                                                                               --                                                                               --                                                                               --                                HPV18                                                                              894      --                                                                               --                                                                               A --                                                                               --                                                                               C C A C --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                HPV33                                                                              856      --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               G --                                                                               A --                                                                               --                                                                               G --                                                                               --                                                                               --                                                                               --                                                                               --                                WD68                                                                               (Seq ID No. 298)                                                                        5'                                                                               C A C A C A A T D Y Y Y A G T G       T                                                                              G                                                                              C                                                                              C C                       WD69                                                                               (Seq ID No. 129)                                                                        5'                                                                               C A C A C A A A G G A C A G G G       T                                                                              G                                                                              T                                                                              T C                       HPV06                                                                              801      5'                                                                               C A C A C T A T G T T T A G T G       T                                                                              T                                                                              C                                                                              C C                       HPV11                                                                              801        --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --      --                                                                             G                                                                              --                                                                             --                                                                               --                      HPV16                                                                              833        --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               T C C --                                                                               --                                                                               --                                                                               --                                                                               --      --                                                                             G                                                                              --                                                                             --                                                                               --                      HPV18                                                                              882        --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               A --                                                                               G A C --                                                                               --                                                                               G --      --                                                                             G                                                                              T                                                                              T --                      HPV33                                                                              844        --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               A --                                                                               --                                                                               C --                                                                               C --                                                                               --      --                                                                             G                                                                              --                                                                             --                                                                               --                      __________________________________________________________________________

The E7 negative strand primers are used as mixtures: WD70 (Seq ID No. 127) and WD71 (Seq ID No. 128); and WD68 (Seq ID No. 263) and WD69 (Seq ID No. 129).

                                      TABLE 6c                                     __________________________________________________________________________     E6 Consensus Negative Strand Primer                                            __________________________________________________________________________     WD67 (Seq ID No. 130)                                                                        W G C A W A T G G A W W G C Y G T C T C                          WD66 (Seq ID No. 131)                                                                        A G C A T G C G G T A T A C T G T      C                                                                       T      C                         WD154                                                                               (Seq ID No. 132)                                                                        T C C G T G T G G T G T G T C G T      C                                                                       C      C                         WD155                                                                               (Seq ID No. 133)                                                                        W S C A W A T G G W W W G Y C G T      C                                                                       Y      C                         WD163                                                                               (Seq ID No. 134)                                                                        W G C A W A T G G A W W G Y Y G T      C                                                                       Y      C                         WD164                                                                               (Seq ID No. 135)                                                                        W S C A W A T G G W D W G Y Y G T      C                                                                       Y      C                         HPV6 286      T G C A T A T G G A T A G C C G C      C                                                                       T      C                         HPV11                                                                               286      --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               G --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               T T --                                                                               T      --                                                                      --     --                        HPV16                                                                               286      A --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T T --                                                                               --                                                                               --                                                                               A T      --                                                                      --     --                        HPV18                                                                               292      A --                                                                               --                                                                               --                                                                               --                                                                               G C --                                                                               --                                                                               T A T A --                                                                               T --                                                                               T      --                                                                      --     --                        HPV31         --                                                                               C --                                                                               G --                                                                               G --                                                                               --                                                                               --                                                                               T G T --                                                                               T --                                                                               --                                                                               T      --                                                                      C      --                        HPV33                                                                               390      --                                                                               C --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T T --                                                                               --                                                                               C T      --                                                                      --     --                        HPV43         A --                                                                               --                                                                               A A --                                                                               C --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               T      --                                                                      G      --                        HPV44         --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               T --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               T T T --     --                                                                      --     --                        HPV56         --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               A --                                                                               A T --                                                                               A T      --                                                                      C      --                        __________________________________________________________________________

The E6 negative strand primers are used as mixtures; WD66 (Seq ID No. 131 ), 5 WD67 (Seq ID No. 130)and WD155(Seq ID No. 133); or WD66(Seq ID No. 131), WD67 (Seq ID No. 130), and WD163 (Seq ID No. 134); WD66 (Seq ID No. 131), WD67 (Seq ID No. 130), and WD164 (Seq ID No. 135), or most preferably, WD66 (Seq ID No. 131), WD67 (Seq ID No. 130), and WD154 (Seq ID No. 132). The negative strand primer WD154 (Seq ID No. 132) was designed to hybridize to HPV31 10 DNA. Amplification of E6 sequences from HPV31 nucleic acids is improved when WD154 (Seq ID No. 132) is included.

Additional E6 consensus negative strand primers located in a region of the gene approximately 50 bp distal from WD66 (Seq ID No. 131), WD67 (Seq ID No. 130), and WD 154 (Seq ID No. 132) are provided below. The primers are used in pairs as shown below and amplify a 300 bp region. The three primer sets shown, WD157/WD160 (Seq ID No. 68/Seq ID No. 69); WD158/WD161 (Seq ID No. 70/Seq ID No. 71); and WD159/WD162 (Seq ID No. 72/Seq ID No. 73), which are HPV18 specific, each correspond to the same genomic HPV region, but they differ in length.

Those skilled in the art will recognize that the E6 consensus primers of the invention amplify a sequence that comprises a portion of E7 DNA.

    ______________________________________                                                Seq ID                                                                         No.     Sequence                                                        ______________________________________                                         WD157  68      TTCTAMTGTWGTTSCATAYACASHATA                                     WD160  69      CCAATGTGTCTCCATACACAGAGTC                                       WD158  70      CTAMTGTWGTTSCATAYACASHATA                                       WD161  71      AATGTGTCTCCATACACAGAGTC                                         WD159  72      TAMTGTWGTTSCATAYACASHATA                                        WD162  73      ATGTGTCTCCATACACAGAGTC                                          ______________________________________                                         Predicted Sizes of Products from E6 Consensus Primers                                 Down-                                                                   URR/E6 stream    Product Size for HPV Type                                     Primer Primer    HPV6    HPV11 HPV16 HPV18 HPV33                               ______________________________________                                         WD72   WD70      770     770   802   844   791                                 and    and                                                                     WD73   WD71                                                                    WD72   WD70      770     770   802   844   791                                 and    and                                                                     WD76   WD71                                                                    WD72   WD70      770     770   802   844   791                                 and    and                                                                     WD77   WD71                                                                    WD72   WD68      758     758   790   832   779                                 and    and                                                                     WD73   WD69                                                                    WD72   WD68      758     758   790   832   779                                 and    and                                                                     WD76   WD69                                                                    WD72   WD68      758     758   790   832   779                                 and    and                                                                     WD77   WD69                                                                    WD72   WD66      243     243   242   242   225                                 and    and                                                                     WD73   WD67                                                                    WD72   WD66      243     243   242   242   225                                 and    and                                                                     WD76   WD67                                                                    WD72   WD66      243     243   242   242   225                                 and    and                                                                     WD77   WD67                                                                    WD72   WD66,     243     243   242   242   225                                 and    WD67,                                                                   WD76   and WD154                                                               ______________________________________                                    

To determine if amplification has occurred using the E6 consensus primers, E6 consensus probes are provided. E6 consensus probes WD136 (5'-GAGGTATWTGAHTITGC [Seq ID No. 297]) and WD135 (5'-GAGATWTATKCATATGC [Seq ID No. 105]) are positive strand oligonucleotides directed to the small E6 amplification product and are used together as a mixture. The E6 consensus probes can also be used as E6 consensus positive strand primers. WD135 (Seq ID No. 105) will hybridize to HPV6 and HPV11 DNA. WD136 (Seq ID No. 297) is complementary to HPV types 16, 18, 33, and 39. When used as E6 consensus primers, the E6 consensus probes are used in the following combinations: WD65 (Seq 1D No. 136) and WD64 (Seq ID No. 139); WD83 (Seq ID No. 137) and WD64 (Seq ID No. 139); and WD84 (Seq ID No. 138) and WD64 (Seq ID No. 139). The E6 consensus probes to two regions are depicted in Table 7.

                                      TABLE 7                                      __________________________________________________________________________     E6 Consensus Probes for E6/E7 Product                                          WD65                                                                               (Seq ID No. 136)                                                                        M G A G A C R G C W W T C C A T W T G                             WD83                                                                               (Seq ID No. 137)                                                                        M G A G A C R G S W W T C C A T W    T                                                                         G                                 WD84                                                                               (Seq ID No. 138)                                                                        M G A G A C R G V W W T C C A T W    T                                                                         G                                 WD64                                                                               (Seq ID No. 139)                                                                        A G A G A C A G T A T A C C G C A    T                                                                         G                                 HPV6                                                                               267      C G A G G C G G C T A T C C A T A    T                                                                         G                                 HPV11                                                                              267      --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               A A --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               C --                                                                               T    --                                                                        --                                HPV16                                                                              266      A --                                                                               --                                                                               --                                                                               A T --                                                                               --                                                                               G A --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --   --                                                                        --                                HPV18                                                                              273      A --                                                                               --                                                                               --                                                                               A --                                                                               A --                                                                               T A T A --                                                                               --                                                                               G C --   --                           HPV33                                                                              271      A --                                                                               --                                                                               --                                                                               A G --                                                                               --                                                                               A A --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T    --                                                                        --                                Consensus Probes for Detection of Small E6 Product                             MY135                                                                              (Seq ID No. 140)                                                                            G A G A T W T A T K C A T A T G C                             HPV6                                                                               225          G A G A T T T A T T C A T A T G  C                            HPV11                                                                              225          --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               G --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               -- --                           MY136                                                                              (Seq ID No. 272)                                                                            G A G G T A T W T G A H T T T G  C                            HPV16                                                                              224          G A G G T A T A T G A C T T T G  C                            HPV18                                                                              231          --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               -- --                           HPV33                                                                              229          --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               T --                                                                               --                                                                               --                                                                               -- --                           HPV39            --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               -- --                           HPV45            --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A --                                                                               --                                                                               --                                                                               -- --                           __________________________________________________________________________

To determine the type of the HPV present in a sample amplified using the E6 consensus primers, E6 type-specific probes are provided. These probes are depicted in Tables 8 and 8A. Using URR/E6 consensus primers comprising positive strand primers of Table 6 with WD70 (Seq ID No. 127) and WD71 (Seq ID No. 128) or WD68 (Seq ID No. 298) and WD69 (Seq ID No. 129), any of the HPV typing probes of Table 8 or Table 8A will be effective. These typing probes am also useful when E1 negative strand primers are used for amplification with the URR/E6 positive strand consensus primers.

                                      TABLE 8                                      __________________________________________________________________________     HPV Typing Probes for Use with E6/E7 Amplified Sequences                           Sequence                       Genome                                      Probe                                                                              ID No.                                                                              Specificity                                                                            Sequence          Position                                    __________________________________________________________________________     WD78                                                                               74   HPV6  5'                                                                               CGAAGTGGACGGACAAGAT                                                                              643                                         WD79                                                                               75   HPV11 5'                                                                               CAAGGTGGACAAACAAGACG                                                                             643                                         WD80                                                                               76   HPV16 5'                                                                               GAACACGTAGAGAAACCCAG                                                                             534                                         WD81                                                                               77   HPV18 5'                                                                               CAACCGAGCACGACAGGA                                                                               530                                         WD82                                                                               78   HPV33 5'                                                                               GAGGTCCCGACGTAGAGAA                                                                              534                                         __________________________________________________________________________

                                      TABLE 8A                                     __________________________________________________________________________     HPV Typing Probes for Use with Small E6 Amplified Sequences                                                       Genome                                      Probe                                                                               Seq ID No.                                                                           Specificity                                                                          Sequence          Position                                    __________________________________________________________________________     WD165                                                                               79    HPV31 AAATCCTGCAGAAAGACCTC                                                                             116                                         WD166                                                                               80    HPV31 CCTACAGACGCCATGTTCA                                           WD167                                                                               81    HPV39 CCTTGCAGGACATTACAATAG                                         WD168                                                                               82    HPV39 CAGACGACCACTACAGCAA                                           WD169                                                                               83    HPV42 GGTGCAAAAAGCACTTAACAG                                         WD102                                                                               84    HPV18 ACAGTATTGGAACTTACAG                                                                              213                                         WD103                                                                               85    HPV16 CAACAGTTACTGCGACG 206                                         WD104                                                                               86    HPV33 GCAGTAAGGTACTGCAC  88                                         WD132                                                                               87    HPV18 GACAGTATTGGAACTTACAG                                                                             213                                         WD133                                                                               88    HPV6  ACACCTAAAGGTCCTGTTTC                                                                             248                                         WD134                                                                               89    HPV11 ACACTCTGCAAATTCAGTGC                                                                             175                                         RR1  90    HPV33 GTACTGCACGACTATGT  96                                         WD171                                                                               91    HPV45 ACAAGACGTATCTATTG                                             WD170                                                                               92    HPV18 GCAAGACATAGAAATAA 178                                         RR2  93    HPV33 ACCTTTGCAACGATCTG 213                                         __________________________________________________________________________

The typing probes of Table 8A are useful for typing a sample amplified using positive strand URR/E6 consensus primers WD76 and WD72 (Seq ID No. 125 and Seq ID No. 124) with WD67 (Seq ID No. 130), WD66 (Seq ID No. 131) and WD154 (Seq ID No. 132); WD157 (Seq ID No. 68) and WD160 (Seq ID No. 69); WD158 (Seq ID No. 70) and WD161 (Seq ID No. 71); WD159 (Seq ID No. 72) and WD162 (Seq ID No. 73); WD66 (Seq ID No. 131) and WD155 (Seq ID No. 133); WD66 (Seq ID No. 131) and WD163 (Seq ID No. 134); and WD66 (Seq ID No. 131) and WD164 (Seq ID No. 135). These primer pairs produce a small E6 amplification product of approximately 250 base pairs in length.

The newly discovered nucleotide sequence of the E6, E7, and part of the E1 region of the JB8 and JB10 isolates is provided below (Seq ID No. 141). The JB8 and JB10 isolates are from an unidentified HPV type that was found in a oral/laryngeal dysplasia. The sequence of the L1 region of the JB10 isolate is provided above.

    __________________________________________________________________________     JB 8 AND 10 E6, E7, and Partial E1 (Seq ID No. 141)                            __________________________________________________________________________       1                                                                               GGATCCCCGG                                                                              GCGAGCTCCA                                                                              CTTCAGTATT                                                                              GCCATACCCG                                                                              CTGTCCGGAA                               51                                                                               CACTGTCCAC                                                                              TGCTCTCCTT                                                                              TTAGCCTGTA                                                                              AATTGTTTAC                                                                              TTCGTCTGTG                               101                                                                              CTCTGCTGAC                                                                              TGTTGCTTTG                                                                              ATTTGTTATG                                                                              TCTTGCAACG                                                                              GGCTGTTCTG                               151                                                                              ACTACCTAGT                                                                              AACTTTCGTT                                                                              TTAATGCACG                                                                              CACTGCCTTC                                                                              TTATTTGCTT                               201                                                                              GTGTTTCTTG                                                                              TGCCTGAAAC                                                                              AATGCCTGCG                                                                              CTACCTGTTG                                                                              CTCTGCCCCA                               251                                                                              TCACTAATAT                                                                              TACTATCATC                                                                              TATAAATCCA                                                                              ATTAGGTCTG                                                                              ATCCTGTATC                               301                                                                              GCTACTATAC                                                                              TCTATTTCAT                                                                              CTTCTAATAT                                                                              TGTGTCTCCT                                                                              GTATGTTTTT                               351                                                                              CTACTATTGC                                                                              TTCTACTGAA                                                                              AACCACCCTG                                                                              TACACCCCAA                                                                              CCCCTCCCCA                               401                                                                              TCTGTACCTT                                                                              CGCAGTCCAT                                                                              TGCAGGTTTA                                                                              GTATGTAGCA                                                                              CACTGGTGGC                               451                                                                              ACACCAAACT                                                                              CACGTCGCCC                                                                              ATCAGCAGCT                                                                              GCTCCACCGC                                                                              TCGGACGTTC                               501                                                                              TGTCGACTGC                                                                              TTAGTACAGC                                                                              TAGCTGCACT                                                                              ATACTATTAC                                                                              ATACACAACA                               551                                                                              TTCCGCTTCT                                                                              ATTCTATAAC                                                                              ACGCTTCTTG                                                                              TTCAGCTTGT                                                                              CTGGCTTGCT                               601                                                                              GGTTACGCAC                                                                              ATTATCTGTT                                                                              TCATCCTCCT                                                                              CTGAGCTGTC                                                                              AAATTGTTCA                               651                                                                              TAGTCCWATT                                                                              GTTCGTAACA                                                                              CTGTAGGTCA                                                                              ATTTCGGGTT                                                                              GCGGCACCAA                               701                                                                              ATCTAATATA                                                                              ACATCCTGTA                                                                              TATTAATTGT                                                                              GTCTCCATGC                                                                              ATTGTTATTT                               751                                                                              ATACTTGTGT                                                                              TTCTGTTGCT                                                                              TCGCGCCTTG                                                                              GTCTCCAGCA                                                                              GTTTGTGCAC                               801                                                                              AACCCTTTCC                                                                              AGTACCCTGC                                                                              TATTTCATGG                                                                              AACCGTCGCT                                                                              TTTCATCCAC                               851                                                                              AATTCTCTGT                                                                              TTTTCTTCCG                                                                              GTCCCAATGG                                                                              TATTTGGCAT                                                                              CTATGACACC                               901                                                                              TTATTAACAA                                                                              ATTATACAAA                                                                              CTTCGTTTAG                                                                              TACGCGCTTC                                                                              CAGTGTTGCA                               951                                                                              CCATACACAG                                                                              ACGATGTGTA                                                                              GCGTCTATAT                                                                              TCTATTATTT                                                                              TTGAATAGAA                              1001                                                                              TATTATACAT                                                                              TTTTTACATG                                                                              CACCATATGC                                                                              ACTATCATTT                                                                              CTATACACTA                              1051                                                                              TTTTTAAATC                                                                              ACATATTGCA                                                                              AAGTTATATA                                                                              CATCTGCCCA                                                                              TTCTAATGTT                              1101                                                                              TTCTTGCAAT                                                                              ATACACACTG                                                                              TACCTGCAAA                                                                              GATTGCAAAG                                                                              GTGTATTCAA                              1151                                                                              AGCTTCACAT                                                                              AGTTCATGTA                                                                              TCGTTCGTGG                                                                              TCTTTCTCTG                                                                              GGATCTTGAA                              1201                                                                              ACATAGCTGT                                                                              TTTTGTGTAT                                                                              GGCTGTGTCT                                                                              TTTACTTTTA                                                                              TATGCACCGT                              1251                                                                              TTTCGG--TTC                                                                             AACCGGAATT                                                                              C                                                         __________________________________________________________________________

E1 Region

The present invention also provides primers that are complementary to sequences in the HPV E1 region. The E1 negative strand primers can be used with E1 positive strand primers to amplify only E1 region sequences or can be used in conjunction with E6/E7 positive strand primers to amplify sequences from E6, E7, E1, and combinations of these three regions. These E1 primers are shown below in Table 9.

                                      TABLE 9                                      __________________________________________________________________________     Seq ID No.                                                                               Sequence                                                             __________________________________________________________________________     E1 POSITIVE STRAND PRIMERS                                                     TYP01                                                                              107   A T G G C K G A Y C C T G M A G G T A C                              TYP02                                                                              108   --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               G A T T C --                                                                               --                                                                               --     --                                                                      --     --                            TYP03                                                                              109   --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               C C T T C --                                                                               --                                                                               --     --                                                                      --     --                            TYP04                                                                              110   T G T A M W G G M T G G T T T T A      T                                                                       G      T                             TYP05                                                                              111   --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               G A      G                                                                       --     --                            TYP06                                                                              112   --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A T      G                                                                       --     --                            E1 NEGATIVE STRAND PRIMERS                                                     TYN01                                                                              113   G T A C C T K C A G G R T C M G C C A T                              TYN02                                                                              114   --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               G A A T C --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                            TYN03                                                                              115   --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               G A A G G --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                            TYN04                                                                              116   A C A T A A A A C C A K C C W K T      A                                                                       C      A                             TYN05                                                                              117   --                                                                               --                                                                               C T C --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                            TYN06                                                                              118   --                                                                               --                                                                               C A T --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --     --                                                                      --     --                            TYN07                                                                              119   T C C A C T T C A G W A T T G C C      A                                                                       T      A                             TYN08                                                                              120   --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               Y A --                                                                               --                                                                               --     --                                                                      --     --                            __________________________________________________________________________

These E1 primers can be used in a variety of embodiments of the present invention. For instance, amplifications wholly within the E1 region can be performed using the following primers: (1) TYP01 (Seq ID No. 107) and TYP02 (Seq ID No. 108) and TYP03 (Seq ID No. 109) with TYN07 (Seq ID No. 119) and TYN08 (Seq ID No. 120); (2) TYP04 (Seq ID No. 110) and TYP05 (Seq ID No. 111) and TYP06 (Seq ID No. 112) with TYN07 (Seq ID No. 119) and TYN08 (Seq ID No. 120). Note that TYP03 (Seq ID No. 109) is similar to both TYP02 (Seq ID No. 108) and TYP01 (Seq ID No. 107) and can be omitted from the amplification.

The E1 region is highly conserved among HPVs, however, and although typing of the sample is possible with an E1 amplification, typing is more readily accomplished when the E1 primers are used in conjunction with E6 or E7 primers, as follows. For instance, one can amplify the E6/E7 region using the following E1 and E6/E7 primers: (1) WD72 (Seq ID No. 124) and WD76 (Seq ID No. 125) with TYN01 (Seq 1D No. 1.13) and TYN02 (Seq ID No. 114) and TYN03 (Seq ID No. 115); (2) WD64 (Seq ID No. 139) and WD65 (Seq ID No. 136) with TYN01 (Seq ID No. 113) and TYN02 (Seq ID No. 114) and TYN03 (Seq ID No. 115); (3) WD72 (Seq ID No. 124) and WD76 (Seq ID No. 125) with TYN04 (Seq ID No. 116) TYN05 (Seq ID No. 117) and TYN06 (Seq ID No. 118); (4) WD64 (Seq ID No. 139) and WD65 (Seq ID No. 136) with TYN04 (Seq ID No. 116) and TYN05 (Seq ID No. 117) and TYN06 (Seq ID No. 118); (5) WD72 (Seq ID No. 124) and WD76 (Seq ID No. 125) with TYN07 (Seq ID No. 119) and TYN08 (Seq ID No. 120); and (6) WD64 (Seq ID No. 139) and WD65 (Seq ID No. 136) with TYN07 (Seq ID No. 119) and TYN08 (Seq ID No. 120). In these latter amplifications, the entire E7 region is amplified. Thus, these amplification products can be detected with the E7 consensus probes depicted below:

    __________________________________________________________________________     TYP09                                                                              Seq ID No. 121                                                                         5'                                                                               G A G C A A T T A G W A G A C                                    TYP12                                                                              Seq ID No. 122                                                                           --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               --                                                                               A R Y --                                                                               --                                                                               --                                   __________________________________________________________________________

The examples provided below merely illustrate the invention and in no way limit the scope of the accompanying claims.

EXAMPLE 1 PCR-Based Detection and Typing of HPV Preparation of Clinical Samples for PCR

The disclosed methods for detecting and typing HPV in a clinical sample are suitable for use with any sample that is suspected of containing HPV nucleic acids. It will be apparent to one of ordinary skill in the art that sample preparation procedures vary according to sample source. Specific examples are provided for sample preparation from a variety of sources.

A. Samples collected in ViraPap™ (Digene Diagnostics, Silver Springs, Md.) collection tubes were digested according to manufacturer's instructions. Samples were handled with extreme care to avoid cross-contamination (Kwok, 1989, Nature 339:237-238). Two hundred microliters of each sample was removed for PCR analysis with a disposable piper, precipitated at -20° C. overnight with 2M ammonium acetate and 70% ethanol, dried, and resuspended in 20 μl TE (10 mM Tris-HCl, pH 7.5, 1 mM EDTA). Two μl and 5 μl aliquots were used for each amplification reaction. ViraPap™ collection tubes containing known amounts of purified human genomic DNA from the K562 cell line (ATCC #CCL243), which does not contain HPV DNA, were processed with each batch of 20 samples to monitor possible contamination in sample processing. The K562 cell line provided a negative control.

B. Freshly collected cells from clinical swabs were suspended in 1 ml of saline, pelleted by centrifugation, and the supernatant discarded. If cell suspensions were to be stored for a period of time before the test, antibiotics were generally added to the suspension (a commercially available antibiotic, such as Fungi Bact Solution, is suitable for this purpose). The cell number was estimated, and if blood was present in the sample, the cells were suspended in 1 ml of TE buffer to lyse the red blood cells and then repelleted. About 10² -10⁴ cells were used for each PCR. The cells were first suspended in 100 μl of buffer containing 50 mM Tris, pH 8.5; 1 mM EDTA; 1% Laureth-12; and 200 μg/ml proteinase K. This mixture was incubated at 55 degrees C. for about 1 hour, and then the proteinase K was heat-inactivated by incubating the mixture at 95 degrees C. for 10 minutes. Aliquots containing 10² -10⁴ cells were used per 100 μl of mixture containing proteinase K treated cells.

C. Cervicovaginal lavage samples were stored frozen in 0.9% saline. For PCR the samples, as 1 ml aliquots, were thawed and mixed gently. Fifty microliters of sample was removed with a disposable pipet and added to 50 μl of 2× digestion solution in a labeled tube. The digestion solution was prepared fresh (1× digestion solution comprises 200 μg/ml proteinase-K, 1% Laureth- 12, 20 mM Tris-HCl pH 8.5, and 0.4 mM EDTA). The samples were incubated for one hour at 55° C., spun briefly, and placed at 95° C. for 10 minutes to heat inactivate the protease. The samples were again spun briefly and 5-10 μl of each sample was added to a PCR mix for a 100 μl PCR reaction.

D. The method of the present invention will often be used to determine whether tissue sections in paraffin contain HPV. To prepare such a tissue section, typically 5-10 μM in width, for use in the present method, the following procedure was employed. The tissue section was extracted twice with 1 ml of octane to remove the paraffin. Each extraction was for about one-half hour. The tissue section was then rinsed twice with 100% ethanol to remove the extracting agent and dried. The section was then suspended in buffer with detergents and proteinase K (200 μg/ml proteinase-K, 1% Laureth-12, 50 mM Tris-HCl pH 8.5, and 1 mM EDTA) at 95° C. for 10 minutes and incubated at 55° C. for 2-4 hours. After heat inactivation of the proteinase K, the suspension was centrifuged to pellet debris, and about 1-20 μl of the supernatant were used for each PCR reaction.

Control DNAs

HPV DNAs used in control amplifications were either recombinant plasmids containing HPVs (6, 11, 16, 18, 31, 33, 39, and 45) or DNA from cell lines containing HPVs (HPV16: SiHa [ATCC No. HTB35] or Caski [ATCC No.CRL 1550]; and HPV 18: HeLa [ATCC No. CCL2]). DNA from the K562 cell line (ATCC No. CCL243) served as an HPV-negative control. Cellular DNA (3 to 15 ng) or plasmid DNA (1-10 pg) was used in control amplifications. Products from these amplifications were used to assess the specificity of type-specific probes.

PCR Protocols

All PCR protocols were carried out using a Perkin-Elmer (Norwalk, Conn.) TC480 Thermal Cycler instrument. A typical reaction mixture contained 50 pmoles each L1 consensus primer MY09 (Seq ID No. 269) and MY11 (Seq ID No. 267); 2.5 units of Taq polymerase; 10 μl of 10× PCR buffer (0.5M KCl; 100 mM Tris, pH 8.5; 40 mM MgCl₂); 0.2 mM of each dNTP; 1-20 μl of each clinical, cell, or paraffin sample; and deionized water to 100 μl. A 100 μl mineral oil overlay was added to each reaction to avoid evaporation. When an amplification control was included in the reaction, 5 picomoles of each β-globin primer (PC04 [Seq ID No. 102] and GH20 [Seq ID No. 104]) was added to the reaction mix.

Because of the extreme sensitivity of PCR, the potential exists for false positive results arising from sample cross-contamination or PCR product carry-over. Extreme care was taken to prevent contamination. Only disposable or positive displacement pipets were used in sample handling and PCR set-up. In addition, pre- and post-PCR samples and reagents were kept separated throughout all stages of the work. The extensive use of negative controls support the conclusion that contamination did not occur at any point in sample handling and all positive results represent true vital presence.

The clinical or cell sample aliquot was added immediately before temperature cycling. Tubes containing the K562 negative control DNA or no added DNA were included. PCR reaction times for use with clinical samples were as follows. The machine was heated to 85° C. before the samples were placed into the machine. The machine was then programmed to execute the following temperature changes: 35 cycles of 60 seconds at 95° C., 60 seconds at 55° C. and 60 seconds at 72° C.; 5 minutes at 72° C.; and then hold at 15° C.

For paraffin sections, the machine was programmed to reach 85° C. and execute temperature changes as follows: forty cycles of 60 seconds at 95° C., 60 seconds at 55° C., and 2 minutes at 72° C.; then 5 minutes at 72° C.; and then hold at 15° C. The MY09 (Seq ID No. 269), MY 11 (Seq ID No. 267) PCR product is less than 600 base pairs; however, if alternative primers were used and the PCR product was expected to be longer than 600 base pairs, the machine was programmed to execute temperature changes as follows: 1 minute at 85° C.; forty cycles of a 50 second ramp to 95° C., 50 seconds at 95° C., a 50 second ramp to 55° C., 50 seconds at 55° C., a 50 second ramp to 72° C., and 2 minutes at 72° C.; 5 minutes at 72° C.; and then hold at 15° C.

Following amplification, 5μl of each completed reaction was electrophoresed on a 7% polyacrylamide gel, ethidium bromide stained, and photographed. Dot blots of each PCR amplification reaction were prepared.

Generic HPV Probe

A generic HPV probe was synthesized from 450 bp L1 PCR fragments of HPV 16 (Caski), HPV 18 (HeLa), PAP238B (a cloned clinical sample identified as HPV31) and a highly divergent, unidentified HPV sequence that was previously isolated and cloned from clinical specimens and is referred to here in as PAP88. PCR amplifications were performed separately using nested primers MY74/MY75 (Seq ID No. 6/Seq ID No. 7) for HPV16; MY76/MY77 (Seq ID No. 8/Seq ID No. 9) for HPV18; MY47/MY48 (Seq ID No. 10/Seq ID No. 11) for PAP88; and MY49/MY50 (Seq ID No. 12/Seq ID No. 13) for. PAP238B. The L1 amplification products were used as the templates for preparing the generic probes. The buffer and enzyme conditions were used as described above except that the final 50 μl PCR contained 50 μM each dNTP, 62.5 pmol (50 μCi) each α-³² P-labeled dNTP, and 20 picomoles of each primer. The mineral oil overlay was omitted and the PCR cycling program was as follows: 30 seconds at 95° C., 30 seconds at 55° C., 1 minute at 72° C. for 25 cycles with a final 5 minute extension at 72° C. The PCR products from identical unlabeled reactions were visualized using electrophoresis and ethidium bromide staining. The labeled ˜400 bp fragments were purified using a G50 Sephadex column, and the cpm of the probes was determined using a scintillation counter. The four probes were denatured at 95° C. for 10 minutes in the presence of sheared salmon sperm DNA, then rapidly cooled in a dry ice/ethanol bath before addition to the hybridization solution. Membranes were hybridized with a mixture of 1.0-1.5×10⁵ cpm/ml of each probe.

Hybridization Analysis of PCR Products

To determine if amplification had occurred the following protocol was used. About 2 μl of each reaction mixture were added to 100 μl of denaturing solution (0.4M NaOH and 25 mM EDTA) for each replicate dot and spotted onto replicate, positively-charged, nylon membranes (such as Genetran 45, Biodyne B Membrane [Pall], or Biotran from ICN) using a dot-blot or slot blot apparatus. The resulting dot was rinsed once with 200 μl of 20×SSC. The membrane was then removed from the blotter, air-dried, and exposed to ultraviolet light (with the DNA facing the light) to covalently attach the DNA to the membrane by using a commercial UV crosslinking apparatus (50 mjoules). Amplified L1 fragments from HPV types 6, 11, 16, 18, 31, 33, 35, 39, and 45 were spotted onto each membrane as positive controls to assess cross-hybridization and optimize exposure times.

The membrane was pre-hybridized at least 30 minutes at 65° C. in a water bath or air incubator. The pre-hybridization solution contained 6×SSC, 5× Denhardt's solution, and 0.1% SDS and 100 μg/ml denatured salmon sperm DNA. Alternatively, the membranes can merely be rinsed with pre-hybridization solution. ³² P-labeled consensus probes (1.0-1.5×10⁵ cpm/ml of hybridization mix) were added to each filter and allowed to hybridize at 55° C. for 60-90 minutes. After the hybridization, the hybridization mix was decanted and the membrane was washed twice for 10 minutes in 2×SSC and 0.1% SDS at 56° C. for the HPV generic and β-globin probes. The membrane was then air-dried and allowed to expose X-ray film from 7 to 48 hours. Background was defined by negative controls which included amplified human genomic DNA.

To determine the HPV type of amplified DNA, PCR reaction mixtures were hybridized to type-specific probes as described above. The only significant difference in the procedure was that the final wash of the filter was done at a temperature very near the T_(m) of the particular type-specific probe. Filters hybridized to different type-specific probes were not washed together. Specifically, membranes were hybridized individually with probes for HPV types 6/11, 16, 18, 31, 33, 39, 45, 51, 52, and 53, and PAP88, PAP155, and PAP251 as listed below. Type-specific oligonucleotide probes were ³² P-labeled using a standard kinase reaction (Maniatis et al. eds. Molecular Cloning, 1982, Cold Spring Harbor, N.Y.). Membranes were prehybridized and hybridized as described above, then washed as follows:

    ______________________________________                                         Seq ID No. Probe     Target    Wash Temperature                                ______________________________________                                         142        MY12      HPV6      57° C.                                   147        MY13      HPV11     57° C.                                   152        MY14      HPV16     59° C.                                   168        WD74      HPV18     59° C.                                   170        WD126     HPV31     57° C.                                   172        WD128     HPV31     57° C.                                   178        MY16      HPV33     57° C.                                   179        MY59      HPV33     57° C.                                   184        MY89      HPV39     58° C.                                   185        MY90      HPV39     58° C.                                   196        MY70      HPV45     59° C.                                   197        MY98      HPV45     59° C.                                   202        MY87      HPV51     58° C.                                   203        MY88      HPV51     58° C.                                   205        MY81      HPV52     57° C.                                   206        MY82      HPV52     57° C.                                   207        MY101     HPV53     58° C.                                   208        MY102     HPV53     58° C.                                   209        MY103     HPV53     58° C.                                   224        MY83      PAP88     58° C.                                   225        MY84      PAP88     58° C.                                   226        MY86      PAP155    58° C.                                   220        MY93      PAP251    58° C.                                   221        MY94      PAP251    58° C.                                   ______________________________________                                    

Autoradiogram exposures that gave an intensity comparable to the generic probe were analyzed using the same standards described above. The sensitivity of this method was 100 copies of cloned HPV16 DNA or 10 HeLa cells containing 100-500 copies of HPV18, per 1 ml collection tube when 2-5% was analyzed.

EXAMPLE 2 Dual Amplification of Archival Samples

A second set of consensus primers was designed to amplify a region of the E6 gene approximately 246 bp in length. These consensus primers were used in addition to the L1 consensus primers described in Example 1. The second set provides a means to generate corroborative HPV typing data and focuses on a gene which is consistently retained and expressed in tumors (Yee et al., 1985, Am. J. Pathol. 116:361-366; Seedorf et al., 1987, EMBO 6:139-144; and Broker et al., In Cancer Cells: Molecular Diagnostics of Human Cancer, vol. 7, Cold Spring Harbor, N.Y., 1989, pp. 197-208).

Archival tissue sections, which included 33 cases of cervical carcinoma, were subjected to PCR amplification with the L1 and E6 primer sets. The resulting products were analyzed by dot blot hybridization with consensus and type-specific oligonucleotide probes to illustrate the efficacy of the two site amplification strategy in the detection and typing of genital HPVs.

Tumor Samples

Sections from 48 paraffin-embedded tissue blocks representing 33 cases of cervical carcinoma and 7 HPV-negative control tissues were acquired from the pathology archives at the University of Amsterdam, the University of California at San Francisco, and the University of California at Davis. The case dates ranged from 1979 to 1988. Five micron sections were cut from tissue blocks with a microtome and the microtome blade was thoroughly cleaned with xylene between each specimen to minimize cross-contamination of samples. Dry sections were transferred to Eppendorf tubes for PCR analysis and immediately adjacent sections were mounted and stained with hematoxylin and eosin for independent histological characterization. Preparation of DNA from tissue sections for PCR was done as described in Example 1.

HPV-negative tissues were interspersed with tumor samples during tissue preparation to detect any possible contamination during sample manipulation. The prepared samples were used immediately for PCR amplification, although storage at -20° C. for up to two weeks resulted in only a nominal loss in specific amplification product yield. Control DNAs, described in Example 1, were included as specified below in the section "Dot Blot Hybridization of PCR Products."

PCR Amplification

L1 and E6 amplification reactions were performed using 1 and 10 μl (0.5% and 5%) of each prepared sample. In addition to HPV-negative and HPV-positive control samples, "no DNA" controls were included during each amplification series to detect contamination during reaction set-up. Furthermore, only positive displacement pipets and disposable pipets were used in the assembly of amplification reactions to minimize possible contamination.

Each L 1 amplification reaction contained 50 pmoles each of the L1 degenerate primers MY11 (Seq ID No. 267) and MY09 (Seq ID No. 269) as described (Example 1 ) and 5 pmoles each of the following β-globin primers:

    ______________________________________                                         GH20   Seq ID No.                                                                               GAAGAGCCAAGGACAGGTAC and                                             104                                                                     PC04   Seq ID No.                                                                               CAACTTCATCCACGTTCACC)                                                105                                                                     ______________________________________                                    

The β-globin were included for the simultaneous amplification of a human δ-globin product of 260 bp which served as an internal control.

The E6 reactions included 10 pmoles WD72 (Seq ID No. 124) and 40 pmoles WD76 (Seq ID No. 125) (the positive strand primers) and 10 pmoles WD66, 40 pmoles WD67 (Seq ID No. 130),and 10pmoles WD154(Seq ID No. 134) (the negative strand primers) in a buffer containing 50 mM KCl, 10 mM Tris (8.3), 4 mM MgCl₂, 200 μM of each dNTP and 2.5 units of the recombinant AmpliTaq® polymerase (manufactured and developed by Hoffmann-La Roche and marketed by Perkin Elmer, Norwalk, Conn.).

Each reaction was subjected to forty amplification cycles in a DNA Thermal Cycler (Perkin Elmer, Norwalk, Conn.) using thermocycle step parameters of 95° C. for 1 minute, 55° C. for 1 minute and 72° C. for 2 minutes. An additional five minutes was included at the final 72° C. elongation cycle. Thirty cycles were used in the amplification of HPV positive control DNA. Amplification products (1/20 of the reaction) were separated by electrophoresis using 7% polyacrylamide gels and visualized by UV illumination following ethidium bromide staining.

Probes

Oligonucleotide probes used for the dot blot hybridizations were labeled to a specific activity of 0.3-1×10⁷ cpm/pmole with α-³² P ATP using T4 polynucleotide kinase (NENuclear/du Pont).

The consensus L1 probe was an equimolar mixture of the following four oligonucleotides corresponding to a conserved region located 50 base pairs (bp) from the 5'end of amplified region:

    __________________________________________________________________________     MY18  Seq ID No. 106                                                                          5'CTGTTGTTGATACTACACGCAGTAC;                                    MY46  Seq ID No. 28                                                                           5'CTGTGGTAGATACCACWCGCAGTAC;                                    MY57  Seq ID No. 26                                                                           5'CTGTGGTAGATACCACACGTAGTAC; and                                WD147 Seq ID No. 27                                                                           5'CTGTAGTGGACACTACCCGCAGTAC.                                    __________________________________________________________________________

L1 type-specific probes were MY12 (Seq ID No. 142) for HPV6, MY13 (Seq ID No. 147) for HPV 11, MY14 (Seq ID No. 152) for HPV16, WD74 (Seq ID No. 168) for HPV18, WD126 (Seq ID No. 170) and WD128 (Seq ID No. 172) for HPV31, MY 16 (Seq ID No. 178) and MY59 (Seq ID No. 179) for HPV33 and MY70 (Seq ID No. 196) for HPV45. MY12 (Seq ID No. 142) and MY13 (Seq ID No. 147) were used together as a mixture to detect both HPV6 and 11. In clinical practice it is not necessary to separate HPV6 and HPV 11 type specific probes because these HPVs are highly related in sequence and in pathogenic potential. HPV6 and HPV 11 are most often associated with benign lesions.

The use of two type specific probes for each HPV type provides additional assurance that all HPV DNAs will be typed correctly including variants, where nucleotide changes in the region of one type specific probe have occurred, will not be mistyped. Probes WD126 (Seq ID No. 170), WD128 (Seq ID No. 172), and WD170 (Seq ID No. 92) were designed using sequence information generated from amplification products of clinical isolates which were subsequently identified as HPV31 and HPV45. WD128 (Seq ID No. 172) and WD126 (Seq ID No. 170) reside in separate domains on the L1 product. WD128 (Seq ID No. 172) detects both HPV31 and a variant referred to as HPV31b. The sequence of the HPV31 b L1 product contains a restriction site not present in the archetypic HPV31. PC03 (Seq ID No. 103) was used to identify the β- globin product according to Example 1.

Oligonucleotide probes designed to distinguish E6 products were: WD 133 (Seq ID No. 88) for HPV6, WD134 (Seq ID No. 89) for HPV11, WD103 (Seq ID No. 85) for HPV16, WD132 (Seq ID No. 87) and WD170 (Seq ID No. 92) for HPV18, WD165 (Seq ID No. 79) and WD166 (Seq ID No. 80) for HPV31, RR1 (Seq ID No. 90) and RR2 (Seq ID No. 93) for HPV33, and WD 171 (Seq ID No. 91 ) for HPV45. The sequence of the HPV45 E6/E7 region was determined from pHPV45 kindly provided by K. Shah (Johns Hopkins University).

Dot Blot Hybridization of PCR Products

Replicate dot blots were prepared using 1/50 (2 μl) of each amplification reaction. Additionally, control reactions (HPV positive SiHa DNA, HPV negative K562, and "no DNA") from each amplification series were included. Two μl of each reaction were denatured in 100 μl of 0.4N NaOH, 25 mM EDTA for each dot, applied to a Gentran 45 membrane (Plasco, Inc), and covalently bound by UV linking using a Stratalinker (Stratagene, Inc.) at 400 (×100) μJoules. The filters were washed in 0.1 × SSC, 0.5% SDS at 60° C. for 30 minutes, followed by prehybridization for 15 minutes at 55° C. with 6× SSC, 5× Denhardt's solution 0.5% SDS, 100 μ/ml single-stranded sheared salmon sperm DNA.

Replicate filters were separately hybridized with ³² P-labeled type-specific and generic oligonucleotide probes (1-200,000 cpm/ml) in 6× SSC, 5× Denhardt's solution 0.5% SDS, 100 μg/ml single-stranded sheared salmon sperm DNA for 1 hour at 55° C. Probes WD170 (Seq ID No. 92) and WD171 (Seq ID No. 91) required hybridization at 45° C.

Filters were rinsed briefly in 2× SSC, 0.1% SDS at room temperature and then twice for 10minutes at 45° C. (WD170 [Seq ID No. 92] and WD171 [Seq ID No. 91]); 50°-52° C. (WD132 [Seq ID No. 87], RR1 [Seq ID No. 90] and RR2 [Seq ID No. 93]), 55°-56° C. (the consensus L1 probe mix, WD103 [Seq ID No. 85], WD132 [Seq ID No. 132], WD165 [Seq ID No. 79], and WD166 [Seq ID No. 60]); 56°-57° C. (MY12/MY13 [Seq ID No. 142/Seq ID No. 147], WD126 [Seq ID No. 170], MY16 [Seq ID No. 178], MY 70 [Seq ID No. 196], and WD133/WD134 [Seq ID No. 88/Seq ID No. 89]); or 58°-59° C. (MY14 [Seq ID No. 152], WD128 [Seq ID No. 172], MY59/MY64 [Seq ID No. 179/Seq ID No. 180], MY70 [Seq ID No. 196], and WD74 [Seq ID No. 168]). The membranes were subjected to autoradiography using Kodak XAR-5 film. L1 and E6 dot blot results were scored independently. The results indicated that for HPV45, MY69 (Seq ID No. 195) may be a preferred type-specific probe, because MY70 (Seq ID No. 196) has some sequence similarity to other HPVs.

Bands of predicted size for E6 or L1 were not detected in reactions from the normal cervical tissues nor an appendix. PCR products of the expected size for an L1 product were observed in all tumor samples with the exception of one of the older samples in the collection. Typing results with the E6 and L1 products were in complete agreement in all cased examined, except for one specimens which failed to produce an L1 PCR product. The single L1-negative specimen found in this study illustrates the value of a strategy based on two site analysis.

Other modifications of the embodiments of the invention described above that are obvious to those of ordinary skill in the areas of molecular biology, medical diagnostic technology, biochemistry, virology, genetics and related disciplines are intended to be within the scope of the accompanying claims.

EXAMPLE 3 Preparation of the Biotinylated Long Probes

In a non-isotopic detection format, Bio-11 (dUTP) (Sigma #B7645) was incorporated into the long L1 probe instead of ³² P dNTP. Subsequent detection of the probe utilized a SA-HRP binding step and development of signal with Amersham's Enhanced ChemiLuminescence (ECL) system.

All reactions contained 2 μl of a 1:100 or 1:1000 dilution of the appropriate MY09/MY11 (Seq ID No. 269/Seq ID No. 267) generated L1 PCR product, 50 mM KCL, 10 mM Tris, pH 8.5, 2.5 units Taq polymerase, 200 μM dATP, dCTP, dGTP, 100 μM dTTP and 100 μM Bio-11 dUTP. The primer and MgCl₂ concentrations varied as follows: MY47 (Seq ID No. 10) and MY48 (Seq ID No. 11), 10 picomoles per primer and 4 mM MgCl₂ ; MY49 (Seq ID No. 12) and MY50 (Seq ID No. 13), 10 picomoles each primer and 6 mM MgCl₂ ; MY74 (Seq 1D No. 6) and MY75 (Seq ID No. 7), 10 picomoles each primer and 4 mM MgCl₂ ; MY76 (Seq ID No. 8) and MY77 (Seq ID No. 9), 50 picomoles each primer and 8 mM MgCl₂. Each reaction was 200 μl in volume with a 100 μl mineral oil overlay. Thermal cycling parameters were 30 seconds at 95° C., 30 seconds at 55° C. and 1 minute at 72° C. with a five minute extension at 72° C. at the end of 30 cycles. The biotinylated PCR product was purified using a G50 Sephadex column (eluted with TE and 0.2% SDS) or an isopropanol, 2M ammonium acetate precipitation. Aliquots of both biotinylated and non-biotinylated long probes were electrophoresed on 7% acrylamide gels, ethidium bromide stained, and photographed under UV light. The non-biotinylated probe migrated further than the biotinylated probe.

The hybridization protocol using biotinylated probes was as described in Example I. Amersham's ECL system was used for detection according to the manufacture's instructions; however, the amount of SA-HRP used at the binding step was titrated for each lot of reagent.

Other modifications of the embodiments of the invention described above, that are obvious to those of ordinary skill in the areas of molecular biology, medical diagnostic technology, biochemistry, virology, genetics, and related disciplines, are intended to be within the scope of the invention and the accompanying claims.

EXAMPLE 4 HPV Typing Assay

An HPV typing assay incorporating detection by probe hybridization in a dot-blot format is described in the protocol below. In the dot blot format, a small portion of the amplified DNA is denatured, applied to nylon membranes, and immobilized. Each membrane is then immersed in a probe solution to allow hybridization to the labeled probe. Replicate membranes are hybridized with either probes for one HPV type or a generic HPV probe. Probes can be radioactively labeled, as described above, or covalently conjugated to horseradish peroxidase (HRP) to provide a means of nonisotopic detection in the presence of a chromogenic or chemiluminescent substrate.

Samples are collected and prepared, and the PCR amplification is carried out essentially as described in Example 1, above. The reaction mixture described in Example 1 is modified by the addition of 5 pmoles of HMB01 (Seq ID No. 95) and 2 units UNG (developed and manufactured by Hoffmann-La Roche and marketed by Perkin Elmer, Norwalk, Conn.), and 0.6 mM dUTP is added in place of 0.2 mM dTTP. No mineral overlay is used. Reactions are carried out in a TC9600 Thermal Cycler (Perkin Elmer, Norwalk, Conn.).

The reaction mixtures are incubated prior to amplification at 50° C. for 2 minutes to allow for UNG-catalyzed degradation of any contaminating oligonucleotide transcripts from previous reactions that contain dUMP. The temperature profile for the amplification reaction consists of 35 cycles of 95° C. for 20 seconds, 55° C. for 30 seconds, and 72° C. for 30 seconds. The reaction mixture is incubated at 72° C. for 5 minutes and then either held at 72° C. or the amplified DNA is denatured immediately.

Generic HPV Probe

A biotinylated generic HPV probe is synthesized as a mixture of 450 base pair PCR amplification products from the amplifications of the L1 region of HPV16 (Caski), HPV 18 (HeLa), HPV51, and PAP88. Separate PCR amplifications are performed using biotinylated primers MY74 (Seq ID No. 6) and MY75 (Seq ID No. 7) for the amplification of HPV16, MY76 (Seq ID No. 8) and MY77 (Seq ID No. 9) for the amplification of HPV 18, MY47 (Seq ID No. 10) and MY48 (Seq ID No. 11 ) for the amplification of PAP88, and CEG03 (Seq ID No. 99) and CEG04 (Seq ID No. for the amplification of HPV51.

DNA from each HPV listed above is amplified using the primers MY09 (Seq ID No. 269) and MY11 (Seq ID No. 267) as described above. A 1:100 to 1:1000 dilution of the amplification products is then used in the type-specific amplifications. The type-specification amplifications are carried out in 100 μl reactions essentially as described in Example 1, above. Each reaction contains the following reagents.

1-2 μl of target nucleic acid

50 mM KCL

10 mM Tris-HCl, pH 8.5

2.5 U Taq*DNA polymerase

200 μM each dATP, dCTP, and dGTP

100 μM dTTP

100 μM dUTP

Additionally, the individual reactions contain primers and MgCl2 at the following concentrations.

HPV 16 amplification reaction

0.1 μM (10 pmol) each MY74 (Seq ID No. 6) and MY75 (Seq ID No. 7) 4 mM MgCl2

HPV 18 amplification reaction

0.5 μM (50 pmol) each MY76 (Seq ID No. 8) and MY77 (Seq ID No. 9)

8 mM MgCl₂

PAP88 amplification reaction

0.1 μM (10 pmol) each MY47 (Seq ID No. 10) and MY48 (Seq ID No. 11)

4 mM MgCl₂

HPV51 amplification reaction

0.5 μM (50 pmol) each CEG03 (Seq ID No. 99) and CEG04 (Seq ID No. 100)

4 mM MgCl₂

The biotinylated amplification products are purified by isopropanol precipitation. To each reaction is added 0.4 volumes 5M ammonium acetate and 2 volumes isopropanol. The amplification product is resuspended in TE buffer. Before hybridization, the probe is denatured at 95° C. for 10 minutes in the presence of 2 mg/ml salmon sperm DNA. The optimal ratio and concentration of probe fragments to be used in the hybridization are determined empirically.

Dot Blot Hybridization Analysis of PCR Products

The amplification product is analyzed by hybridization to probes essentially as described in Example 1. Biodyne B nylon membranes (ICN, Irvine, Calif.) are pretreated by incubating for at least 30 minutes in 0.1× SSPE and 0.5% SDS at 65° C. About 3 μl of each amplification reaction mixture is added to 100 μl of denaturing solution (0.4N NaOH and 25 mM EDTA) and spotted onto a membrane. The resulting dot is rinsed with 400 μl of 20× SSC. Amplified L1 fragments from HPV types 6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 45, 51-59, 68, and clinical samples P88, P155, P238A, P291, and W13B are spotted onto each membrane as positive controls to assess cross-hybridization and optimize exposure times. Duplicate membranes are created for hybridization with probes for each of the HPV types described below and the generic HPV probe.

Membranes are "pre-hybridized" by soaking in hybridization buffer (5× SSPE and 0.1% SDS) at 65° C. for at least 30 minutes. Biotinylated consensus probes are added to each filter and allowed to hybridize at 55° C. for at least 90 minutes. The hybridization mix is decanted and the membrane is washed twice at 56° C. for 10 minutes in 2× SSPE and 0.1% SDS.

The ECL detection protocol (Amersham, Arlington Heights, Ill.) is used for visualization of the hybridized probes. Membranes hybridized to different type-specific probes are treated separately. The membranes are submerged in 250 ml of wash solution containing streptavidin-horseradish peroxidase (SA-HRP) at a concentration of 30 ng/ml for membranes hybridized with the generic probe mix and 40 ng/ml for membranes hybridized with the type-specific probes. The membranes are kept in the solution with gentle agitation at room temperature for 15 minutes to allow binding of the SA-HRP to the biotin probe label. The SA-HRP solution is drained and the membrane is washed twice in a large volume of 2×SSPE and 0.1% SDS with vigorous mixing for 10 minutes. The ECL development is carried out according to the manufacturer's instructions. The membrane is exposed to X-ray film at room temperature for 2 hours.

The HPV type is determined essentially as described in Example 1, except that the type-specific probes listed below are used. The set of type-specific probes listed below are all washed at the same temperature, 56° C.

    ______________________________________                                         HPV Type         Probe    Seq ID No.                                           ______________________________________                                         HPV 6/11         MYB12    142                                                                   MYB13    147                                                                   MYB125   145                                                  HPV 16           MYB95    156                                                                   MYB133   159                                                  HPV 18           MYB130   165                                                                   WDB74    168                                                  HPV 26           MYB186   29                                                                    MYB187   30                                                   HPV 31           MYB92    175                                                                   WD128    172                                                  HPV 33           MYB16    178                                                                   MYB64    180                                                  HPV 35           MYB115   181                                                                   MYB117   183                                                  HPV 39           MYB89    184                                                                   MYB90    185                                                  HPV 40           MYB176   45                                                   HPV 42           MYB34    193                                                                   MYB121   190                                                  HPV 45           MYB69    195                                                                   MYB129   201                                                  HPV 51           MYB87    202                                                                   MYB88    203                                                  HPV 52           MYB81    205                                                                   MYB82    206                                                  HPV 53           MYB102   208                                                                   MYB182   38                                                   HPV 54           MYB160   40                                                                    MYB161   41                                                   HPV 55           MYB151   43                                                                    MYB171   44                                                   HPV 56           MYB197   46                                                                    MYB199   48                                                   HPV 57           MYB154   217                                                                   MYB156   219                                                  HPV 59           MYB123   222                                                                   MYB162   51                                                   Isolate Pap 88   MYB83    224                                                                   MYB178   57                                                   Isolate Pap 155  MYB85    227                                                                   MYB163   58                                                   Isolate Pap 251  MYB94    221                                                                   MYB179   59                                                   Isolate Pap 238A MYB104   228                                                                   MYB106   230                                                  Isolate Pap 291  MYB166   60                                                                    MBY167   61                                                   Isolate W13B     MYB164   64                                                                    MYB165   65                                                   HPV 68           MYB191   66                                                                    MYB194   67                                                   ______________________________________                                    

Nonspecific hybridization to nonspecifically amplified genomic DNA can be assessed using a standard generated from the amplification of a sample consisting of 15,000 spleen cell equivalents. Any signal generated from the unknown sample which is equal to or lower than the signal generated from the spleen cell sample cannot be distinguished from background signal and should not be considered HPV positive.

EXAMPLE 5 Reverse Dot Blot Format

An alternate hybridization format is the reverse dot blot format in which the probes are fixed to discrete locations on a membrane and then the entire membrane is immersed in a solution containing the amplified target DNA to allow hybridization to the membrane-bound probes. The reverse dot blot process is described in copending application Ser. Nos. 197,000 and 347,495; in Saiki et al., 1989, Proc. Natl. Acad. Sci. USA 86:6230-6234; and in the AmpliType DQalpha DNA typing kit developed and manufactured by Hoffmann-La Roche Inc. and available through Perkin Elmer, each of which is incorporated herein by reference.

In one embodiment, the amplification primers are biotinylated, as described in Levenson and Chang, 1989, supra, so that any amplified DNA that hybridizes to the membrane bound probes can be easily detected. Detection is carried out by reacting streptavidin conjugated horseradish peroxidase (SA-HRP) with the amplified DNA hybridized to the fixed probe. The HRP thus becomes bound through the SA-biotin interaction to the amplified DNA and can be used to generate a signal by a variety of well known means, such as the generation of a colored compound, e.g., by the oxidation of tetramethylbenzidine (see U.S. Pat. No. 4,789,630, incorporated herein by reference). Probes are immobilized on a nylon membrane as described in Saiki et al., 1989, supra.

One of skill in the art will recognize that the hybridization and wash conditions must be optimized for each set of probes and targets used. The following conditions are intended as suggested starting conditions to be then optimized.

Amplified PCR products are denatured by heating to 95° C. for 3 to 10 minutes, and 40 μl of the denatured PCR product are added to each probe panel for hybridization. Hybridization is carried out at the hybridization temperature (for example, 56° C.) for 20 minutes in a shaking water bath in a hybridization buffer composed of 0.5× SSC, 0.25% SDS, and 5× Denhardt's solution. The hybridization buffer is replaced with 3 ml of a solution consisting of 25 μl of SA-HRP, developed and manufactured by Hoffmann-La Roche Inc. and commercially available from Perkin Elmer (Norwalk, Conn.), in 3.1 ml of hybridization buffer, and incubated for 20 minutes at 57° C. in a shaking water bath.

Washing is carried out in a wash buffer of 2× SSC and 0.1% SDS. After a brief rinse of the membrane in 10 ml of wash buffer, a 12 minute stringent wash in 10 ml of buffer is done at the hybridization temperature (for example, 56° C.). Another 5 minute room temperature wash is then carried out, followed by a 5 minute wash in 10 ml of 0.1M sodium citrate, pH 5.0.

Chromogen binding is carried out in 5 ml of chromogen solution consisting of 5 ml of 0.1M sodium citrate, 5 μl of 3% hydrogen peroxide, and 0.25 ml of chromogen (TMB, developed and manufactured by Hoffmann-La Roche Inc. and commercially available from Perkin Elmer (Norwalk, Conn.)) for 25-30 minutes at room temperature. Three 10 minute washes in distilled water are carried out at room temperature. A post-wash of 1× PBS at room temperature for 30 minutes can enhance signal quality. During steps in which chromogen is present, the membrane should be shielded from light by an aluminum foil covering. The developed membrane should be photographed for a permanent record.

EXAMPLE 6 Microwell Plate Assay for the Detection of HPV

In this embodiment of the invention, the probes are fixed to a well of a microwell plate and the amplified target DNA is hybridized to the bound probes. As in the previous example, the amplification primers are biotinylated to allow detection of amplified DNA that hybridizes to the bound probes.

The probes are immobilized on the plastic surface of a microwell plate as follows. One hundred μl of a solution of 1M CH3COONH4 containing each probe at a concentration of 0.03-2 nanogram/μl are added into each well of a microwell plate (preferably Immulon II from Dynatech, Chantilly, Va.). The plate is incubated at 37° C. for 10 to 20 hours (overnight) and then rinsed with PBS/EDTA (PBS is 2.68 mM KCL, 137 mM NaCl, 1.47 mM KH2PO4, and 8.03 mM Na2HPO4). The wells are then blocked with protein, such as BSA. Alternatively, probes conjugated to bovine serum albumin (BSA) are allowed to adsorb to the plastic surface of the individual wells. Preferably, 96 well plates available from Corning are used for immobilizing BSA-conjugated probes. Amplification is carried out as described above. One hundred microliters of denaturation solution (0.4M NaOH; 80 mM EDTA and 0.005% Thymol blue) are added to each PCR tube. A new pipette tip is used for each tube. In one embodiment, detection may not be performed immediately, in which case the PCR tubes are stored overnight at 2° C. to 8° C. Because denatured amplification reactions become viscous upon storage at 2° C. to 8° C., tubes are briefly warmed at 25° C. to 30° C. prior to opening.

The appropriate number of eight well microwell plate strips (minimally 2 strips) are removed and set into the microwell plate frame. One hundred μl of hybridization/neutralization buffer was pipetted into each well of the microwell plate. Hybridization/neutralization buffer contains 2.5M NaSCN, 80 mM NaH2PO4, 10 mM NaH2PO4, and 0.125% Tween 20. Before use the pH is checked to be 5.0±0.2.

Using plugged tips with a multi channel pipetter, 25 μl of the denatured amplification reaction from each PCR tube in the tray is pipetted to the corresponding well position in the microwell plate. The plate is covered with the microwell plate lid and gently tapped on the side 10 to 15 times. Wells in which proper reagent pipetting has been done will turn light yellow in color. No change or only a slight change in blue color indicates that excess amplified product has been added. This will not affect the assay results, however. The addition of excess amplified product will increase positive OD values but negative OD values will not be affected. The plate is incubated for 60 minutes at 37° C. to allow hybridization.

Following incubation the plate is washed five times with a 1× PCR wash buffer. A 10× concentrate of PCR wash buffer contains 9.94 grams per liter of sodium phosphate dibasic, 4.41 grams per liter sodium phosphate (monobasic), 3.722 grams per liter EDTA, 87.66 grams per liter sodium chloride, 13.7 grams per liter of Tween 20, and 10 grams per liter of Pro Clin 300 (Rohm and Haas, Philadelphia, Pa.). The pH of the solution is adjusted with phosphoric acid (pH 6.5-7.1 is preferred). Washing of the plate may be performed manually or with an automated microwell plate washer programmed accordingly.

For manual washing the contents of the plate are emptied and tapped dry. Three hundred μl of wash solution are added to each well in the plate being tested, and the plate is allowed to soak for 15 to 30 seconds. The plate is again emptied and tapped dry. This wash process is repeated four additional times.

For an automated microplate washer, the following procedure is used. The contents of the wells are aspirated. The washer is programmed to add 350 microliters of working wash solution to each well in the plate being tested, soak for 30 seconds, and aspirate. The steps are repeated four additional times. The plate is then tapped dry.

Avidin-HRP conjugate is prepared as follows. A diluent is prepared that contains 0.1 molar; 0.25% emulsion 25 (DKS International, Inc., Tokyo, Japan); 1.0% Kathon CG (Rohm and Haas, Philadelphia, Pa.); 0.1% phenol; 1.0% bovine gamma globulin. The pH of the diluent solution is adjusted to 7.3 with concentrated HCl. To this diluent, 10 nM of conjugated avidin (Vector Labs, Burlingame, Calif.) is added. One hundred μl of avidin-HRP conjugate is added to each well in the plate being tested. The plate is then covered and incubated 15 minutes at 37° C. and again washed as described above.

A working substrate is prepared by mixing 2.0 ml of substrate A (3 mM hydrogen peroxide, 6.5 mM citrate, and 0.1% Kathon CG) and 0.5 ml of Substrate B (4.2 mM 3,3', 5,5' tetramethylbenzidine and 40% dimethylformamide) for each multiple of two 8 well microwell plate strips (16 tests). The working substrate is prepared no more than three hours before use and stored away from direct sunlight. One hundred μl of working substrate (substrate A and B mixture) are added to each well of the plate being tested. The plate is then covered and incubated in the dark for 10 minutes at room temperature (20° C. to 25° C.).

One hundred μl of Stop Reagent (5% H₂ SO₄) is added to each well being tested. The absorbance of each well of 450 nanometers is read within one hour of adding the Stop Reagent.

EXAMPLE 7 Detection of Oncogenic vs. Non-Oncogenic HPV Genotypes

An important application of HPV typing is the determination of whether an infected patient is at a low or high risk of developing cervical carcinoma. For this purpose, it is not necessary to determine the specific HPV type, only whether the HPV type is oncogenic or non-oncogenic. The assay described herein differentiates oncogenic HPV types and non-oncogenic types of HPV. The HPV types detected which are currently believed to be oncogenic are types 16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 54, 55, 56, 58, 59, and 68. The HPV types detected which are currently believed to be non-oncogenic are types 6, 11, 26, 40, 42, 43, and 44. The classification of HPV into oncogenic and non-oncogenic categories is preliminary because of the scarcity of data. As more information becomes available, the categories will likely be redefined. It will be clear to one of skill in the art that the exemplified probe panels can be reorganized to accommodate any redefinition of the HPV categories. The assay includes amplification of nucleic acid from all HPV types using consensus primers and subsequent classification of type by hybridization with pools of type-specific probes.

Sample Preparation

Samples are collected with and prepared as described in Example 1.

PCR Amplification

A segment of the L1 region of the HPV genome is amplified in a model 9600 Thermal Cycler, available commercially from Perkin Elmer, Norwalk, Conn., essentially as described in Example 1. The L1 consensus primers MYB09 (Seq ID No. 269), MYB 11 (Seq ID No. 267), and HMB01 (Seq ID No. 95) are biotinylated versions of MY09 (Seq ID No. 269), MY 11 (Seq ID No. 267), and HMB01 (Seq ID No. 95). Reactions are carried out in a 100 μl total reaction volume containing the following reagents:

50 pmols each MYB09 (Seq ID No. 269) and MYB 11 (Seq ID No. 267)

5 pmols of HPV type 51-specific biotinylated primer HMBBO1 (Seq ID No. 95)

10 μl 10×reaction buffer (100 mM Tris-HCL, pH 8.3; and 500 mM KCl)

24 μl MgCl2

0.2 mM each dATP, dCTP, and dGTP

0.6 mM dUTP, 2.5 units Taq* DNA polymerase

2 units UNG*

deionized water

The thermal cycler is preheated to 50° C. The clinical sample is added immediately before temperature cycling. The temperature profile for the amplification reaction is 50° C. for 2 minutes; 35 cycles of 95° C for 20 seconds, 55° C. for 30 72° C. for 30 seconds; and 72° C. for between 5 minutes and overnight. Reaction products should not be allowed to cool to 50° C., because residual. UNG activity may begin to destroy the newly synthesized product. If analysis of the amplified product is to be delayed, the reactions can be stably stored by first incubating at 72° C. for at least 12 hours and then immediately freezing at -20° C.

Amplification with the biotinylated primers MYB09 (Seq ID No. 269) and MYB 11 (Seq ID No. 267) generates a double stranded, 450 base pair product which contains a biotin label at the 5' termini of each strand. Following amplification, the amplified product is denatured by incubation in 100 μl of denaturation buffer (0.4% NaOH, 80 mM EDTA, and 0.005% Tymol Blue) at room temperature for at least 10 minutes.

Detection

The amplified product is detected and classified using type-specific probes. Detection is carried out using a microwell plate format as described in Example 6. Alternatively, detection can be carried out using a reverse dot blot format as described in Example 5. One set of probes is used to detect oncogenic HPV types and a second set of probes is used to detect non-oncogenic HPV types. The microwell plates are coated passively at 3-200 ng/well of each probe.

Each of the type-specific probes shown contains two hybridizing sequences specific to each of the two hypervariable regions in the L1 region. The number of 10 probes which can be attached to a microwell plate is limited; having two hybridizing regions on each probe effectively doubles the number of probes which can be attached to the microwell plate. The two hybridizing regions of most of the probes shown are specific for the same type. However, because of possible problems with secondary structure, each of the type 53/54 probes, TYZ021 (Seq ID No. 247) and TYZ022 (Seq ID No. 248), and the type 51/68 probes, TYZ028 (Seq ID No. 249) and TYZ029 (Seq ID No. 250) contains one hybridizing region for each of the two types. The probe hybridization sequences are provided below.

    __________________________________________________________________________     Linked Oligonucleotide Probes                                                  Probe                                                                               HPV Type                                                                             Seq ID No.                                                                           Sequence                                                      __________________________________________________________________________     TYZ001                                                                              HPV 6/11                                                                             231   CATCCGTAACTACATCTTCCAACAATGAATCCYTCTGTTTTGG                   TYZ002                                                                              HPV 11/40                                                                            232   TCTGTGTCTAAATCTGCTACACCCAAGGTACGGGAGGATCC                     TYZ003                                                                              HPV 26                                                                               233   GCTGACAGGTAGTAGCAGAGTTGCCATAACATCTGTTGTAAGTG                  TYZ004                                                                              HPV 42                                                                               234   GGCTAAGGTAACAACGCCCACTGCAACATCTGGTGAT                         TYZ005                                                                              HPV 16                                                                               235   GATATGGCAGCACATAATGACGTAACATCCCAGGCAATTG                      TYZ006                                                                              HPV 18                                                                               236   GGGCAATATGATGCTACCAATGGATGCTGCACCGGCTGA                       TYZ007                                                                              HPV 31                                                                               237   CCAAAAGCCYAAGGAAGATCTTGCAAACAGTGATACTACATT                    TYZ008                                                                              HPV 33                                                                               238   CACACAAGTAACTAGTGACAGTCCTTTGGAGGTACTGTTTTT                    TYZ009                                                                              HPV 35                                                                               239   CTGCTGTGTCTTCTAGTGACAGATCATCTTTAGGTTTTGGTGC                   TYZ010                                                                              HPV 39                                                                               240   TAGAGTCTTCCATACCTTCTACAGACACTTACAGATACCTACAG                  TYZ011                                                                              HPV 45                                                                               241   ATACTACACCTCCAGAAAAGCGCACAGGATTTTGTGTAGAG                     TYZ013                                                                              HPV 52                                                                               242   CACTTCTACTGCTATAACTTGTACACACCACCTAAAGGAAAGG                   TYZ016                                                                              HPV 55                                                                               243   GTGCTGCTACAACTCAGTCTCCCTGAAAAGGCAAAGCAG                       TYZ017                                                                              HPV 56                                                                               244   GCACAGCTATAACATGTCAACGCAGTTAAGTAAATATGATGCACG                 TYZ018                                                                              HPV 58                                                                               245   AGCACCCCCTAAAGAAAAGGAGACATTATGCACTGAAGTAACTAAG                TYZ019                                                                              HPV 59                                                                               246   GCCAGTTAAACAGGACCCCCTAATGWATACACACCTACCAG                     TYZ021                                                                              HPV 53/54                                                                            247   TTCTACCTTACTGGAAGACTGGCAGCATCCACGCAGGATAG                     TYZ022                                                                              HPV 53/54                                                                            248   GCAACCACACAGTCTATGTCGAATAATGCCCCTGCAAAG                       TYZ028                                                                              HPV 51/68                                                                            249   CCCAACATTTACTCCAAGTAACCATACCGCTATCTGCAATCAG                   TYZ029                                                                              HPV 51/68                                                                            250   CTACTACTGAATCAGCTGTACCTATTAGCACTGCCACTGCTG                    __________________________________________________________________________

Because, in this embodiment, the HPV type is only being classified as one of two groups, oncogenic and non-oncogenic, probes for multiple HPV types may pooled and bound to the same location in the microwell plate. In one embodiment, probes are bound to the microwell plate in two wells, one containing a pool of probes specific for the major oncogenic HPV types, types 16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 54, 55, 56, 58, 59, and 68; and the other containing a pool of probes specific for the major non-oncogenic HPV types, types 6, 11, 26, 40, 42, 43, and 44. In other embodiments, additional wells are utilized to decrease the number of probes per well and increase the number of each probe present to insure adequate sensitivity or to provide more detailed type information. It may be desirable to use an equal amount of each probe to equalize sensitivity across types. In this case, because there are more oncogenic types than non-oncogenic types, more wells are required to detect oncogenic types. For example, if no more than 4 probes are put in each well, 4 wells are required for detection of the oncogenic types and two wells are required for the non-oncogenic types. Ideally, the one-well/pool embodiment described above is used.

In general, it may be possible to bind more probes to a membrane as described in Example 5 than to a microwell plate as described in Example 6. A larger amount of total probe also allows increasing the probe pool size while maintaining a sufficient number of each probe to insure adequate sensitivity. On the other hand, the microwell plates have advantages in lower cost and ease of handling.

EXAMPLE 8 Consensus Probes

Additional consensus probes that hybridize to the L1 region are provided below. These probes may be used to detect amplification products from the amplification of HPV nucleic acid using primers pairs MY09/MY11 (Seq ID No. 269/Seq ID No. 267) or PEG01/PEG02.

    __________________________________________________________________________     Consensus Probes                                                               Probe                                                                               Seq ID No.                                                                           Sequence                                                            __________________________________________________________________________     CEG 14                                                                              251   TTTTGGGAKGTKRAYTTAMARGAAAAGTTTTC                                    CEG 15                                                                              252   TTTTGGRAKGTKRAYTTAAARGAAARRTTTTC                                    CEG 16                                                                              253   GAGGARTWTGATTTRCARTTTATWTTTCA                                       CEG 17                                                                              254   GARGARTWTGATTTRCAGTTTATWTTTCAR                                      CEG 18                                                                              255   ATTTGTTGGYRYAATCARYTRTTTGTTAC                                       CEG 19                                                                              256   ATWTGYTGGGGYAATCARTTRTTTGTTAC                                       CEG 20                                                                              257   TTTTGGGAKGTWAATTTAMWAGAAARRTTTTC                                    CEG 21                                                                              258   TTTTGGRAKGTKRAYTTAAAGGAAARGTTTTC                                    CEG 22                                                                              259   GAAGARTWTGATTTRCAATTTATWTTTCARTTRTGT                                CEG 23                                                                              260   GARGARTWTGATTTACARTTTATWTTTCAR                                      CEG 24                                                                              261   ATWTGTTKGGGMAATCAMYTRTTTGTTAC                                       CEG 25                                                                              262   ATTTGYTGGSRYAATCARTTRTTTGTTAC                                       __________________________________________________________________________

    __________________________________________________________________________     SEQUENCE LISTING                                                               (1) GENERAL INFORMATION:                                                       (iii) NUMBER OF SEQUENCES: 298                                                 (2) INFORMATION FOR SEQ ID NO:1:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 15 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:                                        CCAAACAGTAAGAGC15                                                              (2) INFORMATION FOR SEQ ID NO:2:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                               (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:                                       GGCTGTAGAGGGCTTAGAC19                                                          (2) INFORMATION FOR SEQ ID NO:3:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii ) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:                                        GGTTGAAGCTACAAAATGGGCC22                                                       (2) INFORMATION FOR SEQ ID NO:4:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4:                                        GTAGCGCACCTGGACAGG18                                                           (2) INFORMATION FOR SEQ ID NO:5:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 15 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5:                                        CAGGTAGTGACTCAC15                                                              (2) INFORMATION FOR SEQ ID NO:6:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         ( C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:                                        CATTTGTTGGGGTAACCAAC20                                                         (2) INFORMATION FOR SEQ ID NO:7:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7:                                        TAGGTCTGCAGAAAACTTTTC21                                                        (2) INFORMATION FOR SEQ ID NO:8:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8:                                        TGTTTGCTGGCATAATCAAT20                                                         (2) INFORMATION FOR SEQ ID NO:9:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:9:                                        TAAGTCTAAAGAAAACTTTTC21                                                        (2) INFORMATION FOR SEQ ID NO:10:                                              (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 20 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:10:                                       CATATGCTGGGGTAATCAGG20                                                         (2) INFORMATION FOR SEQ ID NO:11:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:11:                                       CAGGTCTGCAGAAAAGCTGT20                                                         (2) INFORMATION FOR SEQ ID NO:12:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12:                                       TATTTGTTGGGGCAATCAG19                                                          (2) INFORMATION FOR SEQ ID NO:13:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13:                                       CTAAATCTGCAGAAAACTTTT 21                                                       (2) INFORMATION FOR SEQ ID NO:14:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 455 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:14:                                       GCMCAGGGWCATAAYAATGGTATATGTTGGCACAATCAATTGTTTTTAA CAGTTGTAGAT60                ACTACTCGCAGCACCAATCTYTCTGTGTGTGCTTCTACTACTTCTCCTATTCCTAATGAA120                TACACACCTACCAGTTTTAAAGAATATGCCAGACATGTGGRGGAATTTGATTTGCAGTTT180                ATAYTTCAACTGTGTAAAATAAC WTTAACTACAGAGGTAATGTCATACATTCATAATATG240               AATACCACTATTTTGGAGGATTGGAATTTTGGTRTTACACCACCTCCTACTGCTARTTTA300                GTTGACACATACCGTTTTGTTCAATCTGCTGCTGTAACTTGTCAAAAGGACACCGCACCG360                CCAGTTAAACAGGACCCTTATGACAAACTAAAGTTTTGGACTGTAAATCTTAAGGAAAGG420                TTTTCTGCAGATCTTGATCAGTWTCCYYTKGGACG455                                         (2) INFORMATION FOR SEQ ID NO:15:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 450 base pairs                                                      (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:15:                                       GCMCAGGGWCATAAYAATGGTATATGTTGGGGAAATCAGCTATTTTTAACTGTGGTTGAT60                 ACTACCCGTAGTACTAACATGACTTTGTGYG CCACTGCAACATCTGGTGATACATATACA120               GCTGCTAATTTTAAGGAATATTTAAGACATGCTGAAGAATATGATGTGCAATTTATATTT180                CAATTGTGTRAAATAACATTAACTGTTGAAGTTATGTCATATATACACAATATGAATCCT240                AACATA TTAGAGGAGTGGAATGTTGGTGTTGCACCACCACCTTCAGGAACTTTAGAAGAT300               AGTTATAGGTATGTACAATCAGAAGCTATTCGCTGTCAGGCTAAGGTAACAACGCCAGAA360                AAAAAGGATCCTTATTCAGACTTTTCCTTTTGGGAGGTAAATTTATCTGA AAAGTTTTCT420               ACTGATTTAGGATCAGTWTCCYYTKGGACG450                                              (2) INFORMATION FOR SEQ ID NO:16:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 450 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:16:                                       GCMCAGGGWCATAAYAATGGCATATGCTGGGGTAATCAGGTATTTGTTACTGTTGTGGAT60                 ACTACCAGAAGCACCAACATGACTATTAATGCAGCTAAAAGCACATTARCTAAATATGAT120                GCCCGTGAAATCAA TCAATACCTTCGCCATGTGGAGGAATATGAACTACAGTTTGTGTTT180               CAACTTTGTAAAATAACCTTAACTGCAGARGTTATGGCATATTTGCATAATATGAATAAT240                ACTTTATTRGACGATTGGAATATTGGCTTATCCCCACCAGTTGCAACTAGCTTAGAGG AT300               AAATATAGGTATATTAAAAGCACAGCTRTTACAYGTCAGAGGGAACAGCCCCCTGCAGAA360                AAGCAGGATCCCCTGGCTAAATATAAGTTTTGGGAAGTTAATTTACAGGACAGCTTTTCT420                GCAGACCTGGGATCAGTWTCCYYTKGGACG 450                                             (2) INFORMATION FOR SEQ ID NO:17:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 458 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:17:                                       GCMCAGGGWCATAAYAATGGTA TTTGTTGGCATAATCARTTATTTTTAACTGTTGTAGAT60                ACTACTAGAAGCACTAATTTTTCTGTATGTGTAGGTACACAGGCTAGTAGCTCTACTACA120                ACGTATGCCAACTCTAATTTTAAGGAATATTTAAGACATGCAGAAGAGTTTGATTTACAG180                TTTGTTYTTCAGTTATGTAAAATTAGTTTAACTACTGAGGTAATGACATATATACATTCT240                ATGAATTCTACTATATTGGAAGAGTGGAATTTTGGTCTTACCCCACCACCGTCAGGTACT300                TTAGAGGAAACATATAGATATGTAACATCACAKGCTATTA GTTGCCAACGTCCTCAACCT360               CCTAAAGAAACAGAGGACCCATATGCCAAGCTATCCTTTTGGGATGTAGATCTTAAGGAA420                AAGTTTTCTGCAGAATTAGATCAGTWTCCYYTKGGACG458                                      (2) INFORMATION FOR SEQ ID NO:18:                                               (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 452 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:18:                                       GCMCAGGGWCATAAYAATGGTATTTGTTGGGGCAATCAGTTATTTGTTACTGTGGTAGAT60                 ACCAC ACGTAGTACCAATATGTCTGTGTGTGCTGCAATTGCAAACAGTGATACTACATTT120               AAAAGTAGTAATTTTAAAGAGTATTTAAGACATGGTGAGGAATTTGATTTACRATTTATA180                TTTCAGTTATGCAAAATAACATTATCTGCAGACATAATGACATATATTC ACAGTATGAAT240               CCTGCTATTTTGGAAGATTGGAATTTTGGATTGACCACACCTCCCTCAGGTTCTTTAGAG300                GATACCTATAGGTTTGTAACCTCACAGGCCATTACATGTCAAAAARCTGCCCCCCAAAAG360                CCCAAGGAAGATCCATTTAAAGA TTATGTATTTTGGGAGGTTAATTTAAAAGAAAAGTTT420               TCTGCAGATTTAGATCAGTWTCCYYTKGGACG452                                            (2) INFORMATION FOR SEQ ID NO:19:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 412 base pairs                                                     (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:19:                                       TATATGCTGGTTTAATCAATTGTTTGTCACGGTGGTGGATACCACCCGCAGCACCAATTT60                 TACTATTAGTGCTGCTACCAACACCGAATCAGAATATAAACCTACCAATTTTAAGGA ATA120               CCTAAGACATGTGGAGGAATATGATTTGCAGTTTATATTCCAGTTGTGTAAGGTCCGTCT180                GACTCCAGAGGTCATGTCCTATTTACATACTATGAATGACTCCTTATTAGATGAGTGGAA240                TTTTGGTGTTGTGCCCCCTCCCTCCACAAGT TTAGATGATACCTATAGGTACTTGCAGTC300               TCGCGCCATTACTTGCCAAAAGGGGGCCGCCGCCGCCAAGCCTAAGGAAGATCCTTATGC360                TGGCATGTCCTTTTGGGATGTAGATTTAAAGGACAAGTTTTCTACTGATTTG412                        (2) INFORMATION FOR SEQ ID NO:20:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 415 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:20:                                       TATTTGTTGGCATAATCAGTTGTTTGTTACTGTAGTGGACACTACCCGCAGTACTAATTT6 0                AACATTATGTGCCTCTACACAAAATCCTGTGCCAAATACATATGATCCTACTAAGTTTAA120                GCACTATAGTAGACATGTGGAGGAATATGATTTACAGTTTATTTTTCAGTTGTGCACTAT180                TACTTTAACTGCAGAGGTTATGTCATATATCCATAGTATG AATAGTAGTATATTGGAAAA240               TTGGAATTTTGGTGTACCTCCACCACCTACTACAAGTTTAGTGGATACATATCGTTTTGT300                GCAATCCGTTGCTGTTACCTGTCAAAAGGATACTACACCTCCAGAAAAGCAGGATCCATA360                TGATAAATTAAAGT TTTGGACTGTTGACCTAAAGGAAAAATTTTCCTCCGATTTG415                    (2) INFORMATION FOR SEQ ID NO:21:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:21:                                       CTGT GGTAGATACCACACGCAGTAC25                                                   (2) INFORMATION FOR SEQ ID NO:22:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:22:                                       CAGTTGTAGATACTACTCGCAGCAC25                                                    (2) INFORMATION FOR SEQ ID NO:23:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                               (xi) SEQUENCE DESCRIPTION: SEQ ID NO:23:                                      CTGTGGTTGATACTACCCGTAGTAC25                                                    (2) INFORMATION FOR SEQ ID NO:24:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:24:                                       CTGTTGTGGATACTACCAGAAGCAC25                                                    (2) INFORMATION FOR SEQ ID NO:25:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D ) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:25:                                       CTGTTGTAGATACTACTAGAAGCAC25                                                    (2) INFORMATION FOR SEQ ID NO:26:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:26:                                       CTGTGGTAGATACCACACGTAGTAC25                                                    (2) INFORMATION FOR SEQ ID NO:27:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:27:                                       CTGTAGTGGACACTACCCGCAGTAC25                                                    (2) INFORMATION FOR SEQ ID NO:28:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:28:                                       CTGTGGTAGATACCACWCGCAGTAC25                                                    (2) INFORMATION FOR SEQ ID NO:29:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:29:                                       GCTGACAGGTAGTAGCAGAGTT22                                                       (2) INFORMATION FOR SEQ ID NO:30:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:30:                                       GCCATAACATCTGTTGTAAGTG22                                                       (2) INFORMATION FOR SEQ ID NO:31:                                              (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 18 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:31:                                       GAGTGGATGCAGATGCTG18                                                           (2) INFORMATION FOR SEQ ID NO:32:                                               (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 23 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:32:                                       CTAATGGTAAGGTTAGTACTGCG23                                                      (2) INFORMATION FOR SEQ ID NO:33:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:33:                                       CAGCATCTGCATCCACTC18                                                           (2) INFORMATION FOR SEQ ID NO:34:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:34:                                       ACCCAGTGCACCAAAACC 18                                                          (2) INFORMATION FOR SEQ ID NO:35:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:35:                                       CCAAAACCTAAAGATGATCCAT 22                                                      (2) INFORMATION FOR SEQ ID NO:36:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:36:                                       CACCAGGCCCATATAATAACAG 22                                                      (2) INFORMATION FOR SEQ ID NO:37:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 15 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:37:                                       TGTCAGCGCGATGCC 15                                                             (2) INFORMATION FOR SEQ ID NO:38:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:38:                                       GCAACCACACAGTCTA TGTC20                                                        (2) INFORMATION FOR SEQ ID NO:39:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:39:                                       GACTCT TTCCGCAACCACAC20                                                        (2) INFORMATION FOR SEQ ID NO:40:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:40:                                       CAGCATCCACGCAGGATAG19                                                          (2) INFORMATION FOR SEQ ID NO:41:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                               (xi) SEQUENCE DESCRIPTION: SEQ ID NO:41:                                      GAATAATGCCCCTGCAAAG19                                                          (2) INFORMATION FOR SEQ ID NO:42:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (i i) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:42:                                       CAAATACAGATATGTGCAGT20                                                         (2) INFORMATION FOR SEQ ID NO:43:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:43:                                       GTGCTGCTACAACTCAGTCT20                                                         (2) INFORMATION FOR SEQ ID NO:44:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:44:                                       CCCTGAAAAGGCAAAGCAG19                                                          (2) INFORMATION FOR SEQ ID NO:45:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:45:                                       GCTAACCTACTGGAGGACTGG21                                                        (2) INFORMATION FOR SEQ ID NO:46:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:46:                                       GCACAGCTATAACATGTCAACG22                                                       (2) INFORMATION FOR SEQ ID NO:47:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:47:                                       CCTCCACATGTCTAAGGTACTG22                                                       (2) INFORMATION FOR SEQ ID NO:48:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 23 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION:SEQ ID NO:48:                                        CAGTTAAGTAAATATGATGCACG23                                                      (2) INFORMATION FOR SEQ ID NO:49:                                              (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 17 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:49:                                       ACACCSCACCGCCAGTT17                                                            (2) INFORMATION FOR SEQ ID NO:50:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:50:                                       TTAAACAGGACCCTTATGACA21                                                        (2) INFORMATION FOR SEQ ID NO:51:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 23 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:51:                                       CCTAATGWATACACACCTACCAG23                                                      (2) INFORMATION FOR SEQ ID NO:52:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:52:                                       CCCAAGGTACGGAGGATCC 19                                                         (2) INFORMATION FOR SEQ ID NO:53:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:53:                                       GATGGCTTAAACTTTTGGAATG 22                                                      (2) INFORMATION FOR SEQ ID NO:54:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:54:                                       CAATCAGCAGCAATTACATG 20                                                        (2) INFORMATION FOR SEQ ID NO:55:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:55:                                       CATGTAATTGCTGCTGATTG 20                                                        (2) INFORMATION FOR SEQ ID NO:56:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:56:                                       TCCCCACCAGTTGCAACTA G20                                                        (2) INFORMATION FOR SEQ ID NO:57:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:57:                                       CATGTCAGA GGGAACAGCC19                                                         (2) INFORMATION FOR SEQ ID NO:58:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:58:                                       GTTGTGCCCCCTCCCTCCA19                                                          (2) INFORMATION FOR SEQ ID NO:59:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                               (xi) SEQUENCE DESCRIPTION: SEQ ID NO:59:                                      GACATTATGCACTGAAGTAACTAAG25                                                    (2) INFORMATION FOR SEQ ID NO:60:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:60:                                       GGCTAATGAATACACAGCCTC21                                                        (2) INFORMATION FOR SEQ ID NO:61:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:61:                                       TCCTTCCACCAGCCTTGAT19                                                          (2) INFORMATION FOR SEQ ID NO:62:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:62:                                       CGCTATCTGCAGTCCCGTGC20                                                         (2) INFORMATION FOR SEQ ID NO:63:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:63:                                       CTGCAGTCCCGTGCTATTACC21                                                        (2) INFORMATION FOR SEQ ID NO:64:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:64:                                       CTCAATCTGTTGCACAAACA20                                                         (2) INFORMATION FOR SEQ ID NO:65:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:65:                                       TAACCTTGCCCCCCTCAG18                                                           (2) INFORMATION FOR SEQ ID NO:66:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:66:                                       CATACCGCTATCTGCAATCAG21                                                        (2) INFORMATION FOR SEQ ID NO:67:                                              (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 22 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:67:                                       CTACTACTGAATCAGCTGTACC22                                                       (2) INFORMATION FOR SEQ ID NO:68:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 27 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:68:                                       TTCTAMTGTWGTTSCATAYACASHATA27                                                  (2) INFORMATION FOR SEQ ID NO:69:                                               (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:69:                                       CCAATGTGTCTCCATACACAGAGTC25                                                     (2) INFORMATION FOR SEQ ID NO:70:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:70:                                       CTAMTGTWGTTSCATAYACASHATA 25                                                   (2) INFORMATION FOR SEQ ID NO:71:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 23 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:71:                                       AATGTGTCTCCATACACAGAGTC 23                                                     (2) INFORMATION FOR SEQ ID NO:72:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 24 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:72:                                       TAMTGTWGTTSCATAYACASHATA 24                                                    (2) INFORMATION FOR SEQ ID NO:73:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:73:                                       ATGTGTCTCCATACACAGAGTC 22                                                      (2) INFORMATION FOR SEQ ID NO:74:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:74:                                       CGAAGTGGACGGACAAGAT 19                                                         (2) INFORMATION FOR SEQ ID NO:75:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:75:                                       CAAGGTGGAC AAACAAGACG20                                                        (2) INFORMATION FOR SEQ ID NO:76:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:76:                                        GAACACGTAGAGAAACCCAG20                                                        (2) INFORMATION FOR SEQ ID NO:77:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (x i) SEQUENCE DESCRIPTION: SEQ ID NO:77:                                      CAACCGAGCACGACAGGA18                                                           (2) INFORMATION FOR SEQ ID NO:78:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:78:                                       GAGGTCCCGACGTAGAGAA19                                                          (2) INFORMATION FOR SEQ ID NO:79:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:79:                                       AAATCCTGCAGAAAGACCTC20                                                         (2) INFORMATION FOR SEQ ID NO:80:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:80:                                       CCTACAGACGCCATGTTCA19                                                          (2) INFORMATION FOR SEQ ID NO:81:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:81:                                       CCTTGCAGGACATTACAATAG21                                                        (2) INFORMATION FOR SEQ ID NO:82:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:82:                                       CAGACGACCACTACAGCAA19                                                          (2) INFORMATION FOR SEQ ID NO:83:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B ) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:83:                                       GGTGCAAAAAGCACTTAACAG21                                                        (2) INFORMATION FOR SEQ ID NO:84:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:84:                                       ACAGTATTGGAACTTACAG19                                                          (2) INFORMATION FOR SEQ ID NO:85:                                              (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 17 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:85:                                       CAACAGTTACTGCGACG17                                                            (2) INFORMATION FOR SEQ ID NO:86:                                              (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 17 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:86:                                       GCAGTAAGGTACTGCAC17                                                            (2) INFORMATION FOR SEQ ID NO:87:                                               (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:87:                                       GACAGTATTGGAACTTACAG20                                                         (2 ) INFORMATION FOR SEQ ID NO:88:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:88:                                       ACACCTAAAGGTCCTGTTTC 20                                                        (2) INFORMATION FOR SEQ ID NO:89:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:89:                                       ACACTCTGCAAATTCAGTGC 20                                                        (2) INFORMATION FOR SEQ ID NO:90:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:90:                                       GTACTGCACGACTATGT 17                                                           (2) INFORMATION FOR SEQ ID NO:91:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:91:                                       ACAAGACGTATCTATTG 17                                                           (2) INFORMATION FOR SEQ ID NO:92:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:92:                                       GCAAGACATAGAAATAA 17                                                           (2) INFORMATION FOR SEQ ID NO:93:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:93:                                       ACCTTTGCAACG ATCTG17                                                           (2) INFORMATION FOR SEQ ID NO:94:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:94:                                       CG ACCCAATGCAAATTGGTC20                                                        (2) INFORMATION FOR SEQ ID NO:95:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:95:                                       GCGACCCAATGCAAATTGGT20                                                         (2) INFORMATION FOR SEQ ID NO:96:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:96:                                       TGCGACCCAATGCAAATTGG20                                                         (2) INFORMATION FOR SEQ ID NO:97:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:97:                                       CTTGCGACCCAATGCAAATT20                                                         (2) INFORMATION FOR SEQ ID NO:98:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:98:                                       GACCCAATGCAAATTGGTCT20                                                         (2) INFORMATION FOR SEQ ID NO:99:                                              (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:99:                                       CATTTGCTGGAACAATCAG19                                                          (2) INFORMATION FOR SEQ ID NO:100:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 23 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:100:                                      TAAATCTAAAGAAAATCGTTCCT23                                                      (2) INFORMATION FOR SEQ ID NO:101:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:101:                                      GAAGAGCCAAGGACAGGTAC20                                                         (2) INFORMATION FOR SEQ ID NO:102:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:102:                                      CAACTTCATCCACGTTCACC20                                                         (2) INFORMATION FOR SEQ ID NO:103:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A ) LENGTH: 20 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:103:                                      ACACAACTGTGTTCACTAGC20                                                         (2) INFORMATION FOR SEQ ID NO:104:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 20 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:104:                                      GAAGAGCCAAGGACAGGTAC20                                                         (2) INFORMATION FOR SEQ ID NO:105:                                              (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:105:                                      CAACTTCATCCACGTTCACC20                                                         (2) INFORMATION FOR SEQ ID NO:106:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:106:                                      CTGTTGTTGATACTACACGCAGTAC 25                                                   (2) INFORMATION FOR SEQ ID NO:107:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:107:                                      ATGGCKGAYCCTGMAGGTAC 20                                                        (2) INFORMATION FOR SEQ ID NO:108:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:108:                                      ATGGCKGAYGATTCAGGTAC 20                                                        (2) INFORMATION FOR SEQ ID NO:109:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:109:                                      ATGGCKGAYCCTTCAGGTAC 20                                                        (2) INFORMATION FOR SEQ ID NO:110:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:110:                                      TGTAMWGGMTGGTTTTATGT 20                                                        (2) INFORMATION FOR SEQ ID NO:111:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:111:                                      TGTAMWGGMTGGTT TGAGGT20                                                        (2) INFORMATION FOR SEQ ID NO:112:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:112:                                      TGTA MWGGMTGGTTTATGGT20                                                        (2) INFORMATION FOR SEQ ID NO:113:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:113:                                      GTACCTKCAGGRTCMGCCAT20                                                         (2) INFORMATION FOR SEQ ID NO:114:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                               (xi) SEQUENCE DESCRIPTION: SEQ ID NO:114:                                     GTACCTGAATCRTCMGCCAT20                                                         (2) INFORMATION FOR SEQ ID NO:115:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:115:                                      GTACCTGAAGGRTCMGCCAT20                                                         (2) INFORMATION FOR SEQ ID NO:116:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D ) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:116:                                      ACATAAAACCAKCCWKTACA20                                                         (2) INFORMATION FOR SEQ ID NO:117:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:117:                                      ACCTCAAACCAKCCWKTACA20                                                         (2) INFORMATION FOR SEQ ID NO:118:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:118:                                      ACCATAAACCAKCCWKTACA20                                                         (2) INFORMATION FOR SEQ ID NO:119:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:119:                                      TCCACTTCAGWATTGCCATA20                                                         (2) INFORMATION FOR SEQ ID NO:120:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:120:                                      TCCACTTCAGWAYAGCCATA20                                                         (2) INFORMATION FOR SEQ ID NO:121:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 15 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:121:                                      GAGCAATTAGWAGAC15                                                              (2) INFORMATION FOR SEQ ID NO:122:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 15 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:122:                                      GAGCAATTAARYGAC15                                                              (2) INFORMATION FOR SEQ ID NO:123:                                              (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:123:                                      CGGTTSAACCGAAAACGG18                                                           (2) INFORMATION FOR SEQ ID NO:124:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:124:                                      CGGTCGGGACCGAAAACGG19                                                          (2) INFORMATION FOR SEQ ID NO:125:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:125:                                      CGGTTSAACCGAAAMCGG 18                                                          (2) INFORMATION FOR SEQ ID NO:126:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:126:                                      CGGTTCAACCGAAAMCGG 18                                                          (2) INFORMATION FOR SEQ ID NO:127:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:127:                                      GCRCAGATGGGRCACAC 17                                                           (2) INFORMATION FOR SEQ ID NO:128:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:128:                                      GCACACCACGGACACAC 17                                                           (2) INFORMATION FOR SEQ ID NO:129:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:129:                                      CACACAAAGGACAGGG TGTTC21                                                       (2) INFORMATION FOR SEQ ID NO:130:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:130:                                      WGCAWA TGGAWWGCYGTCTC20                                                        (2) INFORMATION FOR SEQ ID NO:131:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:131:                                      AGCATGCGGTATACTGTCTC20                                                         (2) INFORMATION FOR SEQ ID NO:132:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                               (xi) SEQUENCE DESCRIPTION: SEQ ID NO:132:                                     TCCGTGTGGTGTGTCGTCCC20                                                         (2) INFORMATION FOR SEQ ID NO:133:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (i i) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:133:                                      WSCAWATGGWWWGYCGTCYC20                                                         (2) INFORMATION FOR SEQ ID NO:134:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:134:                                      WGCAWATGGAWWGYYGTCYC20                                                         (2) INFORMATION FOR SEQ ID NO:135:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:135:                                      WSCAWATGGWDWGYYGTCYC20                                                         (2) INFORMATION FOR SEQ ID NO:136:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:136:                                      MGAGACRGCWWTCCATWTG19                                                          (2) INFORMATION FOR SEQ ID NO:137:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:137:                                      MGAGACRGSWWTCCATWTG19                                                          (2) INFORMATION FOR SEQ ID NO:138:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:138:                                      MGAGACRGVWWTCCATWTG19                                                          (2) INFORMATION FOR SEQ ID NO:139:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:139:                                      AGAGACAGTATACCGCATG19                                                          (2) INFORMATION FOR SEQ ID NO:140:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 17 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:140:                                      GAGATWTATKCATATGC17                                                            (2) INFORMATION FOR SEQ ID NO:141:                                             (i ) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 1271 base pairs                                                    (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:141:                                      GGATCCCCGGGCGAGCTCCACTTCAGTATTGCCATACCCGCTGTCCGGAACACTGTCCAC60                 TGCTCTCCT TTTAGCCTGTAAATTGTTTACTTCGTCTGTGCTCTGCTGACTGTTGCTTTG120               ATTTGTTATGTCTTGCAACGGGCTGTTCTGACTACCTAGTAACTTTCGTTTTAATGCACG180                CACTGCCTTCTTATTTGCTTGTGTTTCTTGTGCCTGAAACAATGCCTGCGCT ACCTGTTG240               CTCTGCCCCATCACTAATATTACTATCATCTATAAATCCAATTAGGTCTGATCCTGTATC300                GCTACTATACTCTATTTCATCTTCTAATATTGTGTCTCCTGTATGTTTTTCTACTATTGC360                TTCTACTGAAAACCACCCTGTACACCC CAACCCCTCCCCATCTGTACCTTCGCAGTCCAT420               TGCAGGTTTAGTATGTAGCACACTGGTGGCACACCAAACTCACGTCGCCCATCAGCAGCT480                GCTCCACCGCTCGGACGTTCTGTCGACTGCTTAGTACAGCTAGCTGCACTATACTATTAC540                A TACACAACATTCCGCTTCTATTCTATAACACGCTTCTTGTTCAGCTTGTCTGGCTTGCT600               GGTTACGCACATTATCTGTTTCATCCTCCTCTGAGCTGTCAAATTGTTCATAGTCCWATT660                GTTCGTAACACTGTAGGTCAATTTCGGGTTGCGGCACCAAATCTA ATATAACATCCTGTA720               TATTAATTGTGTCTCCATGCATTGTTATTTATACTTGTGTTTCTGTTGCTTCGCGCCTTG780                GTCTCCAGCAGTTTGTGCACAACCCTTTCCAGTACCCTGCTATTTCATGGAACCGTCGCT840                TTTCATCCACAATTCTCTGT TTTTCTTCCGGTCCCAATGGTATTTGGCATCTATGACACC900               TTATTAACAAATTATACAAACTTCGTTTAGTACGCGCTTCCAGTGTTGCACCATACACAG960                ACGATGTGTAGCGTCTATATTCTATTATTTTTGAATAGAATATTATACATTTTTTACATG1 020              CACCATATGCACTATCATTTCTATACACTATTTTTAAATCACATATTGCAAAGTTATATA1080               CATCTGCCCATTCTAATGTTTTCTTGCAATATACACACTGTACCTGCAAAGATTGCAAAG1140               GTGTATTCAAAGCTTCACATAGTTCATGTATCGTTCGT GGTCTTTCTCTGGGATCTTGAA1200              ACATAGCTGTTTTTGTGTATGGCTGTGTCTTTTACTTTTATATGCACCGTTTTCGGNTTC1260               AACCGGAATTC1271                                                                (2) INFORMATION FOR SEQ ID NO:142:                                              (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:142:                                      CATCCGTAACTACATCTTCCA21                                                        ( 2) INFORMATION FOR SEQ ID NO:143:                                            (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:143:                                      CTCCTGAAAAGGAAAAGCCA 20                                                        (2) INFORMATION FOR SEQ ID NO:144:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:144:                                      TGGCTTTTCCTTTTCAGGAG 20                                                        (2) INFORMATION FOR SEQ ID NO:145:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:145:                                      ACAATGAATCCYTCTGTTTTGG 22                                                      (2) INFORMATION FOR SEQ ID NO:146:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:146:                                      ATCGCCTCCMCCAAATG 17                                                           (2) INFORMATION FOR SEQ ID NO:147:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:147:                                      TCTGTGTCTAAATCTGCTACA 21                                                       (2) INFORMATION FOR SEQ ID NO:148:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:148:                                      CACACCTGAAA AAGAAAAACAG22                                                      (2) INFORMATION FOR SEQ ID NO:149:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:149:                                      C TGTTTTTCTTTTTCAGGTGTG22                                                      (2) INFORMATION FOR SEQ ID NO:150:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 23 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi ) SEQUENCE DESCRIPTION: SEQ ID NO:150:                                     CAGAAACCCACACCTGAAAAAGA23                                                      (2) INFORMATION FOR SEQ ID NO:151:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 23 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:151:                                      AGAAACCCACACCTGAAAAAGAA23                                                      (2) INFORMATION FOR SEQ ID NO:152:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:152:                                      CATACACCTCCAGCACCTAA20                                                         (2) INFORMATION FOR SEQ ID NO:153:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:153:                                      TTGTAACCCAGGCAATTGCT20                                                         (2) INFORMATION FOR SEQ ID NO:154:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:154:                                      ACATACACCTCCAGCACCTA20                                                         (2) INFORMATION FOR SEQ ID NO:155:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:155:                                      CATACACCTCCAGCACCTA19                                                          (2) INFORMATION FOR SEQ ID NO:156:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:156:                                      GATATGGCAGCACATAATGAC21                                                        (2) INFORMATION FOR SEQ ID NO:157:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:157:                                      AGTTTCTGAAGTAGATATGGCA22                                                       (2) INFORMATION FOR SEQ ID NO:158:                                             (i) SEQUENCE CHARACTERISTICS:                                                  ( A) LENGTH: 21 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:158:                                      CTGAAGTAGATATGGCAGCAC21                                                        (2) INFORMATION FOR SEQ ID NO:159:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 19 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:159:                                      GTAACATCCCAGGCAATTG19                                                          (2) INFORMATION FOR SEQ ID NO:160:                                              (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:160:                                      TTTGTAACCCAGGCAATTGCT21                                                        (2) INFORMATION FOR SEQ ID NO:161:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:161:                                      GTTTGTAACCCAGGCAATTGCT 22                                                      (2) INFORMATION FOR SEQ ID NO:162:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:162:                                      CAGTCTCCTGTACCTGGG 18                                                          (2) INFORMATION FOR SEQ ID NO:163:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:163:                                      GATGCTGCACCGGCTGAA 18                                                          (2) INFORMATION FOR SEQ ID NO:164:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:164:                                      GCCCAGGTACAGGAGAC 17                                                           (2) INFORMATION FOR SEQ ID NO:165:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:165:                                      GGGCAATATGATGCTACCAAT 21                                                       (2) INFORMATION FOR SEQ ID NO:166:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:166:                                      GTACCTGGGCAAT ATGATG19                                                         (2) INFORMATION FOR SEQ ID NO:167:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:167:                                      TCT CCTGTACCTGGGCAA18                                                          (2) INFORMATION FOR SEQ ID NO:168:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:168:                                      GGATGCTGCACCGGCTGA18                                                           (2) INFORMATION FOR SEQ ID NO:169:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:169:                                      TCAGCCGGTGCAGCATCC18                                                           (2) INFORMATION FOR SEQ ID NO:170:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:170:                                      CCAAAAGCCCAAGGAAGATC20                                                         (2) INFORMATION FOR SEQ ID NO:171:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       ( D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:171:                                      CAAAAGCCCAAGGAAGATC19                                                          (2) INFORMATION FOR SEQ ID NO:172:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:172:                                      TTGCAAACAGTGATACTACATT22                                                       (2) INFORMATION FOR SEQ ID NO:173:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:173:                                      GAGGGAGGTGTGGTCAAT18                                                           (2) INFORMATION FOR SEQ ID NO:174:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:174:                                      AAGAACCTGAGGGAGGT17                                                            (2) INFORMATION FOR SEQ ID NO:175:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:175:                                      CCAAAAGCCYAAGGAAGATC20                                                         (2) INFORMATION FOR SEQ ID NO:176:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 16 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:176:                                      ACCACACCTCCCTCAG16                                                             (2) INFORMATION FOR SEQ ID NO:177:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 19 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:177:                                      ACAGGCCATTACATGTCAA19                                                          (2) INFORMATION FOR SEQ ID NO:178:                                              (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:178:                                      CACACAAGTAACTAGTGACAG21                                                        (2) INFORMATION FOR SEQ ID NO:179:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:179:                                      AAAAACAGTACCTCCAAAGGA2 1                                                       (2) INFORMATION FOR SEQ ID NO:180:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:180:                                      TCCTTTGGAGGTACTGTTTTT 21                                                       (2) INFORMATION FOR SEQ ID NO:181:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:181:                                      CTGCTGTGTCTTCTAGTGACAG 22                                                      (2) INFORMATION FOR SEQ ID NO:182:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:182:                                      TGCACCAAAACCTAAAGATG 20                                                        (2) INFORMATION FOR SEQ ID NO:183:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:183:                                      ATCATCTTTAGGTTTTGGTGC 21                                                       (2) INFORMATION FOR SEQ ID NO:184:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:184:                                      TAGAGTCTTCCATAC CTTCTAC22                                                      (2) INFORMATION FOR SEQ ID NO:185:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:185:                                      CTGTA GCTCCTCCACCATCT20                                                        (2) INFORMATION FOR SEQ ID NO:186:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:186:                                      AGACACTTACAGATACCTACAG22                                                       (2) INFORMATION FOR SEQ ID NO:187:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                               (xi) SEQUENCE DESCRIPTION: SEQ ID NO:187:                                     CACACCAGGCCCATATAAT19                                                          (2) INFORMATION FOR SEQ ID NO:188:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           ( ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:188:                                      CCAAGGTACGGGAGGATC18                                                           (2) INFORMATION FOR SEQ ID NO:189:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:189:                                      GATCCTCCCGTACCTTG17                                                            (2) INFORMATION FOR SEQ ID NO:190:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:190:                                      CACTGCAACATCTGGTGAT19                                                          (2) INFORMATION FOR SEQ ID NO:191:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:191:                                      TCACCAGATGTTGCAGTG18                                                           (2) INFORMATION FOR SEQ ID NO:192:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:192:                                      GGCGTTGTTACCTTAGCC18                                                           (2) INFORMATION FOR SEQ ID NO:193:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:193:                                      GGCTAAGGTAACAACGCC18                                                           (2) INFORMATION FOR SEQ ID NO:194:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:194:                                      GGATACTACACCTCCAG17                                                            (2) INFORMATION FOR SEQ ID NO:195:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 21 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:195:                                      ATACTACACCTCCAGAAAAGC21                                                        (2) INFORMATION FOR SEQ ID NO:196:                                             ( i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:196:                                      TAGTGGACACTACCCGCAG19                                                          (2) INFORMATION FOR SEQ ID NO:197:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:197:                                      GCACAGGATTTTGTGTAGAGG21                                                        (2) INFORMATION FOR SEQ ID NO:198:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:198:                                      TGTATTTGGCACAGGATTTTG 21                                                       (2) INFORMATION FOR SEQ ID NO:199:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:199:                                      CAGGATTTTGTGTAGAGGCA 20                                                        (2) INFORMATION FOR SEQ ID NO:200:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:200:                                      CAAATCCTGTGCCAGGTAC 19                                                         (2) INFORMATION FOR SEQ ID NO:201:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:201:                                      GCACAGGATTTTGTGTAGAG 20                                                        (2) INFORMATION FOR SEQ ID NO:202:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:202:                                      TATTAGCACTGCCACTG CTG20                                                        (2) INFORMATION FOR SEQ ID NO:203:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:203:                                      CCCAACA TTTACTCCAAGTAAC22                                                      (2) INFORMATION FOR SEQ ID NO:204:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:204:                                      CTGAGGTTAGAAAGGAAAGCA21                                                        (2) INFORMATION FOR SEQ ID NO:205:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                               (xi) SEQUENCE DESCRIPTION: SEQ ID NO:205:                                     CACTTCTACTGCTATAACTTGT22                                                       (2) INFORMATION FOR SEQ ID NO:206:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii ) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:206:                                      ACACACCACCTAAAGGAAAGG21                                                        (2) INFORMATION FOR SEQ ID NO:207:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:207:                                      CGCAACCACACAGTCTATGT20                                                         (2) INFORMATION FOR SEQ ID NO:208:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:208:                                      TTCTACCTTACTGGAAGACTGG22                                                       (2) INFORMATION FOR SEQ ID NO:209:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         ( C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:209:                                      GGAGGTCAATTTGCAAAAC19                                                          (2) INFORMATION FOR SEQ ID NO:210:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:210:                                      TGCAGGGGCATTATTCTTT19                                                          (2) INFORMATION FOR SEQ ID NO:211:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 16 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:211:                                      TACAGCATCCACGCAG16                                                             (2) INFORMATION FOR SEQ ID NO:212:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 15 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:212:                                      CACGCAGGATAGCTT15                                                              (2) INFORMATION FOR SEQ ID NO:213:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 16 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:213:                                      CCACGCAGGATAGCTT16                                                             (2) INFORMATION FOR SEQ ID NO:214:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:214:                                      GTGCTGCTACAACTCAGTCT20                                                         (2) INFORMATION FOR SEQ ID NO:215:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:215:                                      GCTACAACTCAGTCTCCATC20                                                         (2) INFORMATION FOR SEQ ID NO:216:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:216:                                      TGCCTTTTCAGGGGGAG 17                                                           (2) INFORMATION FOR SEQ ID NO:217:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:217:                                      AATGTCTCTTTGTGTGCCAC 20                                                        (2) INFORMATION FOR SEQ ID NO:218:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:218:                                      GTGTGCCACTGTAACCACA 19                                                         (2) INFORMATION FOR SEQ ID NO:219:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:219:                                      GGATCAGTAGGGGTCTTAGG 20                                                        (2) INFORMATION FOR SEQ ID NO:220:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 22 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:220:                                      GCACTGAAGTAACTAAGGA AGG22                                                      (2) INFORMATION FOR SEQ ID NO:221:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:221:                                      AGCACCCCC TAAAGAAAAGGA21                                                       (2) INFORMATION FOR SEQ ID NO:222:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:222:                                      GCCAGTTAAACAGGACCC18                                                           (2) INFORMATION FOR SEQ ID NO:223:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                               (xi) SEQUENCE DESCRIPTION: SEQ ID NO:223:                                     CATAAGGGTCCTGTTTAACTG21                                                        (2) INFORMATION FOR SEQ ID NO:224:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 23 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:224:                                      ATTAATGCAGCTAAAAGCACATT23                                                      (2) INFORMATION FOR SEQ ID NO:225:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:225:                                      GATGCCCGTGAAATCAATCAA21                                                        (2) INFORMATION FOR SEQ ID NO:226:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:226:                                      TACTTGCAGTCTCGCGCCA19                                                          (2) INFORMATION FOR SEQ ID NO:227:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 23 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:227:                                      CCAACACCGAATCAGAATATAAA23                                                      (2) INFORMATION FOR SEQ ID NO:228:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 23 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:228:                                      GTAGGTACACAGGCTAGTAGCTC23                                                      (2) INFORMATION FOR SEQ ID NO:229:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:229:                                      GCTCTACTACAACGTATGCCA21                                                        (2) INFORMATION FOR SEQ ID NO:230:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:230:                                      AGTTGCCAACGTCCTCAAC19                                                          (2) INFORMATION FOR SEQ ID NO:231:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 43 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:231:                                      CATCCGTAACTACATCTTCCAACAATGAATCCYTCTGTTTTGG43                                  (2) INFORMATION FOR SEQ ID NO:232:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 41 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:232:                                      TCTGTGTCTAAATCTGCTACACCCAAGGTACGGGAGGATCC41                                    (2) INFORMATION FOR SEQ ID NO:233:                                              (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 44 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:233:                                      GCTGACAGGTAGTAGCAGAGTTGCCATAACATCTGTTGTAAGTG44                                  (2) INFORMATION FOR SEQ ID NO:234:                                            (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 37 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:234:                                      GGCTAAGGTAACAACGCCCACTGCAACATCTGGTGAT 37                                       (2) INFORMATION FOR SEQ ID NO:235:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 40 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:235:                                      GATATGGCAGCACATAATGACGTAACATCCCAGGCAATTG 40                                    (2) INFORMATION FOR SEQ ID NO:236:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 39 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:236:                                      GGGCAATATGATGCTACCAATGGATGCTGCACCGGCTGA 39                                     (2) INFORMATION FOR SEQ ID NO:237:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 42 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:237:                                      CCAAAAGCCYAAGGAAGATCTTGCAAACAG TGATACTACATT42                                  (2) INFORMATION FOR SEQ ID NO:238:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 42 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:238:                                      CACACAAGTAACTAGTGACA GTCCTTTGGAGGTACTGTTTTT42                                  (2) INFORMATION FOR SEQ ID NO:239:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 43 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:239:                                      CTGCTGTGTC TTCTAGTGACAGATCATCTTTAGGTTTTGGTGC43                                 (2) INFORMATION FOR SEQ ID NO:240:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 44 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:240:                                       TAGAGTCTTCCATACCTTCTACAGACACTTACAGATACCTACAG44                                (2) INFORMATION FOR SEQ ID NO:241:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 41 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (x i) SEQUENCE DESCRIPTION: SEQ ID NO:241:                                     ATACTACACCTCCAGAAAAGCGCACAGGATTTTGTGTAGAG41                                    (2) INFORMATION FOR SEQ ID NO:242:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 43 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:242:                                      CACTTCTACTGCTATAACTTGTACACACCACCTAAAGGAAAGG43                                  (2) INFORMATION FOR SEQ ID NO:243:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 39 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:243:                                      GTGCTGCTACAACTCAGTCTCCCTGAAAAGGCAAAGCAG39                                      (2) INFORMATION FOR SEQ ID NO:244:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 45 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:244:                                      GCACAGCTATAACATGTCAACGCAGTTAAGTAAATATGATGCACG45                                (2) INFORMATION FOR SEQ ID NO:245:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 46 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:245:                                      AGCACCCCCTAAAGAAAAGGAGACATTATGCACTGAAGTAACTAAG46                               (2) INFORMATION FOR SEQ ID NO:246:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 41 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:246:                                      GCCAGTTAAACAGGACCCCCTAATGWATACACACCTACCAG41                                    (2) INFORMATION FOR SEQ ID NO:247:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 41 base pairs                                                      (B ) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:247:                                      TTCTACCTTACTGGAAGACTGGCAGCATCCACGCAGGATAG41                                    (2) INFORMATION FOR SEQ ID NO:248:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 39 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:248:                                      GCAACCACACAGTCTATGTCGAATAATGCCCCTGCAAAG39                                      (2) INFORMATION FOR SEQ ID NO:249:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 43 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:249:                                      CCCAACATTTACTCCAAGTAACCATACCGCTATCTGCAATCAG43                                  (2) INFORMATION FOR SEQ ID NO:250:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 42 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:250:                                      CTACTACTGAATCAGCTGTACCTATTAGCACTGCCACTGCTG42                                   (2) INFORMATION FOR SEQ ID NO:251:                                              (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 32 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:251:                                      TTTTGGGAKGTKRAYTTAMARGAAAAGTTTTC32                                             (2 ) INFORMATION FOR SEQ ID NO:252:                                            (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 32 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:252:                                      TTTTGGRAKGTKRAYTTAAARGAAARRTTTTC 32                                            (2) INFORMATION FOR SEQ ID NO:253:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 29 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:253:                                      GAGGARTWTGATTTRCARTTTATWTTTCA 29                                               (2) INFORMATION FOR SEQ ID NO:254:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 30 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:254:                                      GARGARTWTGATTTRCAGTTTATWTTTCAR 30                                              (2) INFORMATION FOR SEQ ID NO:255:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 29 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:255:                                      ATTTGTTGGYRYAATCARYTRTTTGTTAC 29                                               (2) INFORMATION FOR SEQ ID NO:256:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 29 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:256:                                      ATWTGYTGGGGYAATCARTTRT TTGTTAC29                                               (2) INFORMATION FOR SEQ ID NO:257:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 32 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:257:                                      TTTTGGGAKGTW AATTTAMWAGAAARRTTTTC32                                            (2) INFORMATION FOR SEQ ID NO:258:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 32 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:258:                                      TT TTGGRAKGTKRAYTTAAAGGAAARGTTTTC32                                            (2) INFORMATION FOR SEQ ID NO:259:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 36 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:259:                                      GAAGARTWTGATTTRCAATTTATWTTTCARTTRTGT36                                         (2) INFORMATION FOR SEQ ID NO:260:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 30 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:260:                                      GARGARTWTGATTTACARTTTATWTTTCAR30                                               (2) INFORMATION FOR SEQ ID NO:261:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 29 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:261:                                      ATWTGTTKGGGMAATCAMYTRTTTGTTAC29                                                (2) INFORMATION FOR SEQ ID NO:262:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 29 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:262:                                      ATTTGYTGGSRYAATCARTTRTTTGTTAC29                                                (2) INFORMATION FOR SEQ ID NO:263:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:263:                                      GATCAGTWTCCYYTKGGACG20                                                         (2) INFORMATION FOR SEQ ID NO:264:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:264:                                      GATCAGTTTCCYYTKGGACG20                                                         (2) INFORMATION FOR SEQ ID NO:265:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 18 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:265:                                      CCGTTTTCGGTTSAACCG18                                                           (2) INFORMATION FOR SEQ ID NO:266:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 19 base pairs                                                       (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:266:                                      CCGTTTTCGGTCCCGACCG19                                                          (2) INFORMATION FOR SEQ ID NO:267:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A ) LENGTH: 20 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:267:                                      GCMCAGGGWCATAAYAATGG20                                                         (2) INFORMATION FOR SEQ ID NO:268:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 20 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:268:                                      GCMCAGGGDCAYAAYAATGG20                                                         (2) INFORMATION FOR SEQ ID NO:269:                                              (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:269:                                      CGTCCMARRGGAWACTGATC20                                                         (2) INFORMATION FOR SEQ ID NO:270:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 20 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:270:                                      CGTCCMARRGGAWAYTGATC 20                                                        (2) INFORMATION FOR SEQ ID NO:271:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 25 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:271:                                      CTGTGGTAGATACCACTCGCAGTAC 25                                                   (2) INFORMATION FOR SEQ ID NO:272:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:272:                                      GAGGTATWTGAHTTTGC 17                                                           (2) INFORMATION FOR SEQ ID NO:273:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 467 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:273:                                      GAGCTCGCACAGGGTCATAACAATGGTATCTGTT GGGGCAATCAATTGTTTGTTACCTGT60                GTTGATACCACCCGCAGTACTAACCTTACCATTAGTACATTATCTGCAGCATCTGCATCC120                ACTCCATTTAAACCATCTGATTATAAACAATTTATAAGACATGGCGAAGAATATGAATTA180                CAATTTATA TTTCAGTTGTGTAAAATAACACTTACAACAGATGTTATGGCTTACATACAT240               TTAATGAATGCCTCCATATTGGAGGATTGGAATTTTGGACTAACCTTACCTCCCACTGCT300                AGTTTGGAAGATGCCTATAGGTTTATTAAAAACTCTGCTACTACCTGTCAGC GTAACGCC360               CCTCCTGTGCCAAAGGAAGATCCTTTTCAAAAATTTAAATTTTGGGATGTAGATTTAAAA420                GAAAAATTTTCTATTGATTTGGATCAGTTTCCCCTGGGACGAAGCTT467                             (2) INFORMATION FOR SEQ ID NO:274:                                             (i) SEQUENCE CHARACTERISTICS:                                                   (A) LENGTH: 461 base pairs                                                    (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:274:                                      GAGCTCGCCCAGGGTCATAATAATGGCATCTGTTGGAACAATCAGTTATTTGTAACTGTT60                 GTGGATACCACCAGGAA TACAAACATGACACTTTCTGCAACCACACAGTCTATGTCCACA120               TATAATTCAAAGCAAATTAAACAGTATGTTAGACATGCAGAGGAATATGAATTACAATTT180                GTGTTTCAACTATGTAAAATATCCCTGTCTGCTGAGGTTATGGCCTATTTACATACTATG 240               AATTCTACCTTACTGGAAGACTGGAATATAGGTTTGTCGCCTCCTGTTGCCACTAGCTTA300                GAGGACAAATACAGATATGTAAAAAGTGCAGCTATAACCTGTCAAAAGGATCAGCCCCCT360                CCTGAAAAGCAGGACCCACTATCTAAATATAAATT TTGGGAGGTCAATTTACAAAACAGT420               TTTTCTGCTGATTTGGATCAGTATCCCCTGGGACGAAGCTT461                                   (2) INFORMATION FOR SEQ ID NO:275:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 467 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                        (D) TOPOLOGY: linear                                                          (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:275:                                      GAGCTCGCCCAGGCTCATAATAATGGTATTTGTTGGTTTAATGAATTGTTTGTAACCGTT60                 GTGGATACCACCCGCAGTACTAATGTAACCATTTGTACTGCTACATCCCCCCCTGTATCT120                 GAATATAAAGCCACGAGCTTTAGGGAATATTTGCGCCATACAGAAGAGTTTGATTTGCAA180               TTCATTTTTCAGTTATGTAAAATACATTTAACCCCTGAAATTATGGCCTACCTACATAAT240                ATGAATAAAGCCTTGTTGGATGACTGGAACCTTGGTGTGGTAC CTCCACCCTCTACCAGT300               CTAGAAGACACATATAGGTTTTTGCAGTCCAGAGCTATTACATGTCAGAAGGGTGCTGCT360                GCCCCGCCGCCCAAGGAGGATCGCTATGCCAAATTATCATTTTGGACTGTTGATTTACGA420                GACAAGTTCTCCACTGAT TTGGATCAGTATCCCTTGGGACGAAGCTT467                            (2) INFORMATION FOR SEQ ID NO:276:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 467 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:276:                                      GAGCTCGC ACAGGGACATAACAATGGCATTTGTTGGGGCAACCAATTGTTTGTTACTTGT60                GTAGATACTACCCGCAGTACCAACCTCACTATTAGTACTGTATCTGCACAATCTGCATCT120                GCCACTTTTAAACCATCAGATTATAAGCAGTTTATAAGGCATGGTGAGGAA TATGAATTA180               CAGTTTATATTTCAATTGTGTAAAATTACTCTTACCACTGATGTAATGGCCTATATCCAT240                ACAATGAATTCTGCTATTTTGGAAAATTGGAATTTTGGCCTTACCTTGCCTCCTACTGCT300                AGTTTGGAAGATGCATATAGGTTTAT TAAAAATTCAGCTACTACATGTCAACGCGATGCC360               CCTGCACAGCCCAAGGAGGATCCATTTAGTAAATTAAAATTTTGGGACGTTGATCTTAAA420                GAAAAGTTTTCTATTGATTTAGATCAGTATCCCCTTGGACGAAGCTT467                              (2) INFORMATION FOR SEQ ID NO:277:                                            (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 460 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:277:                                      GAGCTCGCCCAGGGTCATAATAATGGTCTTTAAAAGTGAAAGAGGGAGGCAGAAGAAGGT 60                GTGATAGTATAGGGATGTAAAGAAGACTCAACCAGCCCTTGCTGGTTTTGAAGCTGGAAG120                AGGGTCGTGAGCCAAGGAATAAGGGCAGCCTCTAAAAAGCTGGAAAAGATCAGAAAATGG180                TTCTCACCTACAGTCTCCAGAAAGGAACACCGTC TGGCCAACACCTTGATCTTAGCCCAG240               TGAGACTCATTTCTACCTTCTGACTTCCAGAAGTTTAAGGTAATCAACTTTTGTTGTTTT300                AAGCCACTGAGTTAATGGCAATTTGTTACAACAGCCATAGCAAGCTAGTATACCGAGTCT360                CATTCTTAC CCTTATGAGACCTTCCACAATTTCATCCCATCCAACCCACCCAGCAATGTC420               TTCTGCTTGGGTCAGATCAGTATCCCTTTGGACGAAGCTT460                                    (2) INFORMATION FOR SEQ ID NO:278:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 461 base pairs                                                     ( B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:278:                                      GAGCTCGCACAGGGACATAATAATGGTATATGCTGGGGTAATCAACTATTTGTTACTGTT60                 GTAGACACTACACGTAGTACCAACATGACTTTATGTTCTGAG GAAAAATCAGAGGCTACA120               TACAAAAATGAAAACTTTAAGGAATACCTTAGACATGTGGAAGGATATGATTTGCAGTTT180                ATATTTCAGCTGTGCAAAATATCCCTTACTGCAAATGTTATGCAATACATACACACCATG240                AATCCAGATATATTAGA GGACTGGCAATTTGGCCTTACACCACCTCCTTCAGGTAATTTA300               CAGGACACATATAGATTTGTTACCTCGCAGGCTATTACCTGTCAAAAAACATCCCCTCCA360                ACAGCAAAGGAAGATCCTCTTAAAAAGTACAGTTTTTGGGAAATCAATTTAAAGGAAAAA 420               TTTTCTGCAGATTTAGATCAGTATCCCCTTGGACGAAGCTT461                                   (2) INFORMATION FOR SEQ ID NO:279:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 394 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:279:                                      ACACTACACGTAGTACTAATTTACATTGTCTGCCTGCACCGAAACAGCCGTACCTGCTGT60                 ATATAGCCCTACAAAGTTTAAGGAATATACTAGGCATGTGGAGGAATATGATTTACAATT120                TATATTTCAATTGTGTACTATCACA TTAACTGCAGACGTTATGGCCTACATCCATACTAT180               GAATCCTACAATTTTGGACAATTGGAATATAGGCGTTACCCCTCCACCATCTGCAAGCTG240                AGCTTGGTGGACACGTATAGGTATTTACAATCAGCAGCATAGCATGTCAGAAGGATGCTC300                 CTGCACCTGAAAAAAAGGGTCCCTATGACGATTTAAAATTTTGGAATGTTGATTTAAAGG360               AAAAGTTTAGTAACAGAACTAGATCAGTATCCCC394                                          (2) INFORMATION FOR SEQ ID NO:280:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 467 base pairs                                                      (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:280:                                      GAGCTCGCACAGGGACATAATAATGGCATTTCGTGGAATAATCACGTTTTTATTACTTGT60                 GTTGACACTCATAGAATGACCAATTTAACCATT ACGACTCGTGTTACTCAATCTGTTGCA120               CAAACATTTACTCCAGCAAACTTTAAGCAATACATTAGGCATGGGGAAGAATATGAATTG180                CAATTTATATTTCAATTGTGTAAAATCACTTTAACTACTGAAATTATGGCTTACCTGCAC240                ACCATGGA TTCTACAATTTTAGAACAGTGGAATTTTGGATTAACCTTGCCCCCCTCAGCT300               AGTTTGGAGGAGTCCTATGCATTTGTAAAAAATGCAGCAACATCCTGTCACAAGGACAGT360                CCTCCACAGGCTAAACAAGACCCTTTGGCAAAATATAAATTTTGGAATGTA GACCTTAAG420               GAACGCTTTTCTTTGGATTTGGATCAGTTTCCTTTTGGACGAAGCTT467                             (2) INFORMATION FOR SEQ ID NO:281:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 462 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:281:                                      GAGCTCGCACAGGGGTCATAATAATGGCATATGCTGGGGTAATCAGGTATTTGTTACTGT60                 TGTGGATACTACCAGAAGCACCAACATGACTATTAATGCAGCTAAAAGCACATTAACTAA120                ATATGATGCCCGTGAA ATCAATCAATACCTTCGCCATGTGGAGGAATATGAACTACAGTT180               TGTGTTTCAACTTTGTAAAATAACCTTAACTGCAGAAGTTATGGCATATTTGCATAATAT240                GAATAATACTTTATTAGACGATTGGAATATTGGATTATCCCCACCAGTTGCAACTAGCTT 300               AGAGGATAAATATAGGTATATTAAAAGCACAGCTATTACATGTCAGAGGGAACAGCCCCC360                TGCAGAAAAGCAGGATCCCCTGGCTAAATATAAGTTTTGGGAAGTTAATTTACAGAACAG420                CTTTTCTGCAGACCTGGATCAGTTTCCTTTTGGA CGAAGCTT462                                 (2) INFORMATION FOR SEQ ID NO:282:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 464 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:282:                                      GAGCTCGCCCAGGGACATAATAAT GGCATTTGTTGGTTTAATGAGTTATTTGTTACAGTT60                GTAGATACTACCCGCAGTACCAATATTACTATTTCAGCTGCTGCTACACAGGCTAATGAA120                TACACAGCCTCTAACTTTAAGGAATACCTCCGCCACACCGAGGAATATGACTTACAGGTT180                ATATTGCAACTTTGCAAAATACATCTTACCCCTGAAATTATGGCATACCTACATAGTATG240                AATGAACATTTATTGGATGAGTGGAATTTTGGCGTGTTACCACCTCCTTCCACCAGCCTT300                GATGATACCTATCGCTATCTGCAGTCCCGTGCTATTACCTGC CAAAAGGGTCCTTCCGCC360               CCTGCCCCTAAAAAGGATCCTTATGATGGCCTTGTATTTTGGGAGGTTGATTTAAAGGAC420                AAACTATCCACAGATTTGGATCAGTATCCTTTGGGACGAAGCTT464                                (2) INFORMATION FOR SEQ ID NO:283:                                              (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 467 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:283:                                      GAGCTCGCACAGGGTCATAATAATGGTATTTGTTGGCATAATCAATTATTTCTTACTGTT60                 GTGGATA CCACTCGCAGTACCAATTTTACTTTGTCTACTACTACTGAATCAGCTGTACCA120               AATATTTATGATCCTAATAAATTTAAGGAATATATTAGGCATGTTGAGGAATATGATTTG180                CAATTTATATTTCAGTTGTGTACTATAACATTGTCAACTGATGTAATGTC CTATATACAT240               ACTATGAATCCTGCTATTTTGGATGATTGGAATTTTGGTGTTGCCCCTCCACCATCTGCT300                AGTCTTGTAGATACATACCGCTATCTGCAATCAGCAGCAATTACATGTCAAAAAGACGCC360                CCTGCACCTACTAAAAAGGATCCAT ATGATGGCTTAAACTTTTGGAATGTAAATTTAAAA420               GAAAAGTTTAGTTCTGAACTGGATCAGTTTCCCCTTGGACGAAGCTT467                             (2) INFORMATION FOR SEQ ID NO:284:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 464 base pairs                                                     (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:284:                                      CAACGTGCACAAGGCCATAATAATGGTATTTGTTGGAGTAACCAATTGTTTGTTACTGTA60                 GTTGATACAACCCGTAGTACAAATATGTCTGTGTGTTCTGCTGTGTCTTCTAGTGACAG T120               ACATATAAAAATGACAATTTTAAGGAATATTTAAGGCATGGTGAAGAATATGATTTACAG180                TTTATTTTTCAGTTATGTAAAATAACACTAACAGCAGATGTTATGACATATATTCATAGT240                ATGAACCCGTCCATTTTAGAGGATTGGAATTTT GGCCTTACACCACCGCCTTCTGGTACC300               TTAGAGGACACATATCGCTATGTAACATCACAGGCTGTAACTTGTCAAAAACCCAGTGCA360                CCAAAACCTAAAGATGATCCATTAAAAAATTATACTTTTTGGGAGGTTGATTTAAAGGAA420                AAGTTTTC TGCAGACTTAGATCAATTTCCGTTGGGCCGTAAATT464                               (2) INFORMATION FOR SEQ ID NO:285:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 467 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:285:                                      GAGCTCGCCCAGGGTCATAATAATGGTATATGTTGGCATAATCAATTATTTCTTACTGTT60                 GTGGACACTACCCGTAGTACCAACTTTACATTATCTACCTCTATAGAGTCTTCCATACCT120                TCTACATATGATCCTTCTAAGTTTAAGGAATATACCAGGCA CGTGGAGGAGTATGATTTA180               CAATTTATATTTCAACTGTGTACTGTCACATTAACAACTGATGTTATGTCTTATATTCAC240                ACTATGAATTCCTCTATATTGGACAATTGGAATTTTGCTGTAGCTCCTCCACCATCTGCC300                AGTTTGGTAGACACTT ACAGATACCTACAGTCTGCAGCCATTACATGTCAAAAGGATGCT360               CCAGCACCTGAAAAGAAAGATCCATATGACGGTCTAAAGTTTTGGAATGTTGACTTAAGG420                GAAAAGTTTAGTTTGGAACTTGATCAGTATCCCTTGGGACGAAGCTT 467                            (2) INFORMATION FOR SEQ ID NO:286:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 467 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:286:                                      CAAAAGGCCCAGGGCCATAACAATGGCATATGTTTTGGCAATCAGTTATT TGTTACAGTT60                GTAGACACCACTCGTAGCACTAATTTGACCTTATGTGCTGCCACACAGGGCCCCACACCA120                GGCCCATATAATAACAGTAATTTCAAGGAATATTTGCGTCAGGGGGAGGAGTTTGATTTG180                CAGTTTATTTTTCAGTTATGTGTA ATTACCTTAAATGCAGAGGTTATGACATATATTCAT240               GCAATGGATCCTACGTTGTTGGAGGATTGGAACTTTAAAATTGCTCCTCCAGCCTCTGCA300                TCCTTAGAGGATACATATAGGTTCCTTACCAACAAGGCTATTGCCTGTCAGCGCGATGCC360                GCCCCCAAGGTACGGGAGGATCCATATAAAAAATATAAATTTTGGGATGTCAATTTAACA420                GAAAGATTTTCTTCCCAATTAGATCAATTTCCATTAGGACGTAAGTT467                             (2) INFORMATION FOR SEQ ID NO:287:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 461 base pairs                                                      (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:287:                                      GAGCTCGCACAGGGTCATAATAATGGTATATGTTGGGGAAATCAGCTATTTTTAACTGTG60                 GTTGATACTACCCGTAGTACTAACATGACTTT GTGTGCCACTGCAACATCTGGTGATACA120               TATACAGCTGCTAATTTTAAGGAATATTTAAGACATGCTGAAGAATATGATGTGCAATTT180                ATATTTCAATTGTGTAAAATAACATTAACTGTTGAAGTTATGTCATATATACACAATATG240                AATCCTA ACATATTAGAGGAGTGGAATGTTGGTGTTGCACCACCACCTTCAGGAACTTTA300               GAAGATAGTTATAGGTATGTACAATCAGAAGCTATTCGCTGTCAGGCTAAGGTAACAACG360                CCAGAAAAAAAGGATCCTTATTCAGACTTTTCCTTTTGGGAGGTAAATTT ATCTGAAAAG420               TTTTCTACTGATTTAGATCAGTATCCTCTGGGACGAAGCTT461                                   (2) INFORMATION FOR SEQ ID NO:288:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 467 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:288:                                      GAGCTCGCACAGGGTCATAACAATGGTATTTGTTGGCATAATCAGTTGTTTGTTGCTGTA60                 GTGGACACTACCCGCAGTACTAATTTAACATTATGTGCCTCTACACAAAATCCTGTGCCA120                AGTACATATGACCCT ACTAAGTTTAAGCAGTATAGTAGACATGTGGAGGAATATGATTTA180               CAGTTTATTTTTCAGTTGTGCACTATTACTTTAACTGCAGAGGTTATGTCATATATCCAT240                AGTATGAATAGTAGTATATTAGAAAATTGGAATTTTGGTGTCCCTCCACCACCTACTAC A300               AGTTTGGTGGATACATATCGTTTTGTGCAATCAGTTGCTGTTACCTGTCAAAAGGATACT360                ACACCTCCAGAAAAGCAGGATCCATATGATAAATTAAAGTTTTGGACTGTTGACCTAAAG420                GAAAAATTTTCCTCCGATTTGAATCAGTATCCC TTGGGACGAAGCTT467                            (2) INFORMATION FOR SEQ ID NO:289:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 449 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:289:                                      TCCACCGTGCGCAGGGTCACAAT AATGGCATTTGCTGGAACAATCAGCTTTTTATTACCT60                GTGTTGATACTACCAGAAGTACAAATTTAACTATTAGCACTGCCACTGCTGCGGTTTCCC120                CAACATTTACTCCAAGTAACTTTAAGCAATATATTAGGCATGGGGAAGAGTATGAATTGC180                AATTTATTTTTCAATTATGTAAAATTACTTTAACTACAGAGGTAATGGCTTATTTACACA240                CAATGGATCCTACCATTCTTGAACAGTGGAATTTTGGATTAACATTACCTCCGTCTGCTA300                GTTTGGAGGATGCATATAGGTTTGTTAGAAATGCAGCTACT AGCTGTCAAAAGGACACCC360               CTCCACAGGCTAAGCCAGATCCTTTGGCCAAATATAAATTTTGGGATGTTGATTTAAAGG420                AACGATTTTCTTTAGATTTAGACCAATTT449                                               (2) INFORMATION FOR SEQ ID NO:290:                                              (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 461 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:290:                                      GAGCTCGCCCAGGGTCATAATAATGGCATATGTTGGGGCAATCAGTTGTTTGTCACAGTT60                 GTGGAT ACCACTCGTAGCACTAACATGACTTTATGTGCTGAGGTTAGAAAGGAAAGCACA120               TATAAAAATGAAAATTTTAAGGAATACCTTCGTCATGGCGAGGAATTTGATTTACAATTT180                ATTTTTCAATTGTGCAAAATTACATTAACAGCTGATGTTATGACATACAT TCATAAGATG240               GATGCCACTATTTTAGAGGACTGGCAATTTGGCCTTACCCCACCACCGTCTGCATCTTTG300                GAGGACACATACAGATTTGTCACTTCTACTGCTATAACTTGTCAAAAAAACACACCACCT360                AAAGGAAAGGAAGATCCTTTAAAG GACTATATGTTTTGGGAGGTGGATTTAAAAGAAAAG420               TTTTCTGCAGATTTAAATCAGTATCCTTTTGGACGAAGCTT461                                   (2) INFORMATION FOR SEQ ID NO:291:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 461 base pairs                                                     (B) TYPE: nucleic acid                                                          (C) STRANDEDNESS: single                                                      (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:291:                                      GAGCTCGCCCAGGGTCATAATAATGGCATCTGTTGGAACAATCAGTTATTTGTAACTGTT60                 GTGGATACCACCAGGAATACAAACATGACTCTTTCCGCAACCACACAGTCTATGTCTA CA120               TATAATTCAAAGCAAATTAAACAGTATGTTAGACATGCAGAGGAATATGAATTACAATTT180                GTGTTTCAACTATGTAAAATATCCCTGTCTGCTGAGGTTATGGCCTATTTACATACTATG240                AATTCTACCTTACTGGAAGACTGGAATACAGG TTTGTCGCCTCCTGTTGCCACTAGCTTA300               GAGGACAAATACAGATATGTGAAAAGTGCAGCTATAACCTGTCAAAAGGATCAGCCCCCT360                CCTGAAAAGCAGGACCCACTATCTAAATATAAATTTTGGGAGGTCAATTTGCAAAACAGT420                TTTTCTG CTGATTTGGATCAGTATCCCCTGGGACGAAGCTT461                                  (2) INFORMATION FOR SEQ ID NO:292:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 464 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:292:                                      GAGCTCGCACAGGGTCATAATAATGGTATTTGTTGGGGCAATCAATTGTTTTTAACAGTT60                 GTAGATACCACCCGTAGTACTAACCTAACATTGTGTGCTACAGCATCCACGCAGGATAGC120                TTTAATAATTCTGACTTTAGGGAGTATATTAGACATGTGG AGGAATATGATTTACAGTTT180               ACATTTCAGTTATGTACCATAGCCCTTACAGCAGATGTTATGGCCTATATTCATGGAATG240                AATCCCACTATTCTAGAGGACTGGAACTTTGGTATAACCCCCCCAGCTACAAGTAGTTTG300                GAGGACACATATAGG TTTGTACAGTCACAGGCCATTGCATGTCAAAAGAATAATGCCCCT360               GCAAAGGAAAAGGAGGATCCTTACAGTAAATTTACTTTTTGGACTGTTGACCTTAAGGAA420                CGATTTTCATCTGACCTTGATCAGTATCCCCTTGGACGAAGCTT 464                               (2) INFORMATION FOR SEQ ID NO:293:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 455 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:293:                                      GCGCAGGGCCACAATAATGGTATTTGTTGGGGGAATCAGTTATTTGTTA CTGTTGTAGAT60                ACTACACGTAGTACAAACATGACAATATGTGCTGCTACAACTCAGTCTCCATCTACAACA120                TATAATAGTACAGAATATAAACAATACATGCGACATGTTGAGGAGTTTGACTTACAGTTT180                ATGTTTCAATTATGTAGTATTAC CTTAACTGCTGAGGTAATGGCCTATTTACATACCATG240               AATCCTGGTATTTTGGAACAGTGGAACTTTGGGTTGTCGCCACCCCCAAATGGTACCTTA300                GAAGACAAATACAGATATGTGCAGTCACAGGCCATTACATGTCAAAAGCCTCCCCCTGAA360                AAGGCAAAGCAGGACCCCTATGCAAAATTAAGTTTTTGGGAGGTAGATCTCAGAGAAAAG420                TTTTCTAGTGAGTTAGATCAATATCCCCTTGGTAG455                                         (2) INFORMATION FOR SEQ ID NO:294:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 461 base pairs                                                      (B) TYPE: nucleic acid                                                        (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:294:                                      GAGCTCGCACAGGGACATAATAATGGCATTTGCTGGGGTAATCAATTATTTGTGACTGTA60                 GTAGATACTACTAGAAGTACTAACATGACTA TTAGTACTGCTACAGAACAGTTAAGTAAA120               TATGATGCACGAAAAATTAATCAGTACCTTAGACATGTGGAGGAATATGAATTACAATTT180                GTTTTTCAATTATGCAAAATTACTTTGTCTGCAGAGGTTATGGCATATTTACATAATATG240                AATGCT AACCTACTGGAGGACTGGAATATTGGGTTATCCCCGCCAGTGGCCACCAGCCTA300               GAAGATAAATATAGATATGTTAGAAGCACAGCTATAACATGTCAACGGGAACAGCCACCA360                ACAGAAAAACAGGACCCATTAGCTAAATATAAATTTTGGGATGTTAACTT ACAGGACAGT420               TTTTCTACAGACCTGGATCAGTATCCCTTGGGACGAAGCTT461                                   (2) INFORMATION FOR SEQ ID NO:295:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 449 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                            (ii) MOLECULE TYPE: DNA (genomic)                                             (xi) SEQUENCE DESCRIPTION: SEQ ID NO:295:                                      GCCCAGGGACATAACAATGGCATGTGCTGGGGCAATCGGATCTTCCTAACAGTGGTGGAC60                 ACCACGCGCAGCACAAATGTCTCTTTGTGTGCCACTGTAACCACAGAAACTAATTATAAA120                GCCTCCAATTATAA GGAATACCTTAGGCATATGGAGGAATATGATTTGCAGTTCATTTTT180               CAACTGTGCAAAATAACACTCACCCCCGAGATAATGGCATACATACATAACATGGATGCG240                CGGTTGCTAGAGGACTGGAACTTTGGTGTCCCCCCACCCCCGTCCGCCAGCCTGCAGG AC300               ACCTACAGGTATTTGCAATCCCAAGCGATAACATGTCAGAAGCCCACACCCCCTAAGACC360                CCTACTGATCCCTATGCAACCATGACATTCTGGGATGTGGATCTCAGTGAAAGTTTTTCC420                ATGGATCTGGACCAATTCCCCCTGGGACG 449                                              (2) INFORMATION FOR SEQ ID NO:296:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 464 base pairs                                                     (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:296:                                      CACAAGGCTCAGGGTTTAAACA ATGGTATATGTTGGCACAATCAATTGTTTTTAACAGTT60                GTAGATACTACTCGCAGCACCAATCTTTCTGTGTGTGCTCTACTACTCTCTATTCCTAAT120                GTATACACACCTACCAGTTTTAAAGAATATGCCAGACATGTGGAGGAATTTGATTTGCAG180                TTTATATTTCAACTGTGTAAAATAACATTAACTACAGAGGTAATGTCATACATTCATAAT240                ATGAATACCACTATTTTGGAGGATTGGAATTTTGGTGTTACACCACCTCCTACTGCTAGT300                TTAGTTGACACATACCGTTTTGTTCAATCTGCTGCTGTAA CTTGTCAAAAGGACACCGCA360               CCGCCAGTTAAACAGGACCCTTATGACAAACTAAAGTTTTGGCCTGTAGATCTTAAGGAA420                AGGTTTTCTGCAGATCTTGATCAGTTTCCTTTGGGACGTAAATT464                                (2) INFORMATION FOR SEQ ID NO:297:                                              (i) SEQUENCE CHARACTERISTICS:                                                 (A) LENGTH: 17 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:297:                                      GAGGTATWTGAHTTTGC17                                                            (2) INFORMATION FOR SEQ ID NO:298:                                             (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 21 base pairs                                                      (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (xi) SEQUENCE DESCRIPTION: SEQ ID NO:298:                                      CACACAATDYYYAGTGTGCCC 21                                                       __________________________________________________________________________ 

We claim:
 1. A purified oligonucleotide probe, wherein said probe consists of a nucleotide sequence which hybridizes to a nucleic acid from a human papillomavirus (HPV) type under sequence-specific, stringent hybridization conditions and does not hybridize to a nucleic acid from HPV types 6, 11, 16, 18, and 33 under said conditions, and wherein said probe is chosen from the group consisting ofMYB186 (Seq ID No. 29), MYB187 (Seq ID No. 30), MYB188 (Seq ID No. 31), MYB189 (Seq ID No. 32), MYB202 (Seq ID No. 33), and sequences fully complementary thereto, which hybridize to HPV-26; WD126 (Seq ID No. 170), WD127 (Seq ID No. 171), WD128 (Seq ID No. 172), MY109 (Seq ID No. 173), MY110 (Seq ID No. 174)), WD165 (Seq ID No. 79), WD166 (Seq ID No. 80) and sequences fully complementary thereto, which hybridize to HPV-31; MY92 (Seq ID No. 175), MY127 (Seq ID No. 176), MY128 (Seq ID No. 177), and sequences fully complementary thereto, which hybridize to HPV-31 and HPV-31 B; MY115 (Seq ID No. 181), MY116 (Seq ID No. 182), MY117 (Seq ID No. 183), MYB168 (Seq ID No. 34), MYB169 (Seq ID No. 35), and sequences fully complementary thereto, which hybridize to HPV-35; MY89 (Seq ID No. 184), MY90 (Seq ID No. 185), MY91 (Seq ID No. 186), WD167 (Seq ID No. 81), WD168 (Seq ID No. 82), and sequences fully complementary thereto, which hybridize to HPV-39; MY118 (Seq ID No. 187), MY119 (Seq ID No. 188), MY120 (Seq ID No. 189), MYB174 (Seq ID No. 36), MYB175 (Seq ID No. 37), MYB176 (Seq ID No. 52), and sequences fully complementary thereto, which hybridize to HPV-40; MY33 (Seq ID No. 192), MY34 (Seq ID No. 193), MY121 (Seq ID No. 190), MY122 (Seq ID No. 122), WD169 (Seq ID No. 83), and sequences fully, complementary thereto, which hybridize to HPV-42; MY68 (Seq ID No. 194), MY69 (Seq ID No. 195), MY70 (Seq ID No. 196), MY98 (Seq ID No. 197), MY99 (Seq ID No. 198), MY100 (Seq ID No. 199), MY108 (Seq ID No. 200), MY129 (Seq ID No. 201), WD171 (Seq ID No. 91), and sequences fully complementary hereto, which hybridize to HPV-45; MY87 (Seq ID No. 202), MY88 (Seq ID No. 203), and sequences fully complementary thereto, which hybridize HPV-51; MY80 (Seq ID No. 204), MY81 (Seq ID No. 205), MY82 (Seq ID No. 206), and sequences fully complementary thereto, which hybridize to HPV-52; MY101 (Seq ID No. 207), MY102 (Seq ID No. 208), MY103 (Seq ID No. 209), MYB182 (Seq ID No. 38), MYB159 (Seq ID No. 39), and sequences fully complementary thereto, which hybridize to HPV-53; MY111 (Seq ID No. 210), MY112 (Seq ID No. 211), MY113 (Seq ID No. 212), MY114 (Seq ID No. 213), MYB160 (Seq ID No. 40), MYB161 (Seq ID No. 41), and sequences fully complementary thereto, which hybridize to HPV-54; MYB170 (Seq ID No. 42), MYB151 (Seq ID No. 43), MYB171 (Seq ID No. 44), MY151 (Seq ID No. 43), MY152 (Seq ID No. 215), MY153 (Seq ID No. 216), and sequences fully complementary thereto, which hybridize to HPV-55; MYB196 (Seq ID No. 45), MYB197 (Seq ID No. 46), MYB198 (Seq ID No. 47), MYB199 (Seq ID No. 48), and sequences fully complementary thereto, which hybridize to HPV-56; MY154 (Seq ID No. 217), MY155 (Seq ID No. 218), MY156 (Seq ID No. 219), and sequences fully complementary thereto, which hybridize to HPV-57; MY93 (Seq ID No. 220), MY94 (Seq ID No. 221), MY179 (Seq ID No. 59), and sequences fully complementary thereto, which hybridize HPV-58; MY123 (Seq ID No. 222), MY124 (Seq ID No. 223), MYB172 (Seq ID No. 49), MYB173 (Seq ID No. 50), MYB162 (Seq ID No. 51), and sequences fully complementary thereto, which hybridize to HPV-59; and MYB191 (Seq ID No. 66), MYB192 (Seq ID No. 53), MYB193 (Seq ID No. 54), MYB194 (Seq ID No. 67), MYB195 (Seq ID No. 55), and sequences fully complementary thereto, which hybridize to HPV-68.
 2. A probe of claim 1, wherein said HPV type is HPV-26, and wherein said probe is selected from the group of probes consisting of MYB186 (Seq ID No. 29), MYB187 (Seq ID No. 30), MYB188 (Seq ID No. 31), MYB189 (Seq ID No. 32), MYB202 (Seq ID No. 33), and sequences fully complementary thereto.
 3. A probe of claim 1, wherein said HPV type is HPV-31 or HPV-31 B, and wherein said probe is selected from the group of probes consisting of WD126 (Seq ID No. 170), WD127 (Seq ID No. 171), WD128 (Seq ID No. 172), MY109 (Seq ID No. 173), MY110 (Seq ID No. 174), MY92 (Seq ID No. 175), MY127 (Seq ID No. 176), MY128 (Seq ID No. 177), WD165 (Seq ID No. 79), WD166 (Seq ID No. 80), and sequences fully complementary thereto.
 4. A probe of claim 1, wherein said HPV type is HPV-35, and wherein said probe is selected from the group of probes consisting of MY 115 (Seq ID No. 181), MY116 (Seq ID No. 182), MY 117 (Seq ID No. 183), MYB168 (Seq ID No. 34), MYB169 (Seq ID No. 35), and sequences fully complementary thereto.
 5. A probe of claim 1, wherein said HPV type is HPV-39, and wherein said probe is selected from the group of probes consisting of MY89 (Seq ID No. 184), MY90 (Seq ID No. 185), MY91 (Seq ID No. 186), WD167 (Seq ID No. 81), WD168 (Seq ID No. 82), and sequences fully complementary thereto.
 6. A probe of claim 1, wherein said HPV type is HPV-40, and wherein said probe is selected from the group of probes consisting of MY 118 (Seq ID No. 187), MY 119 (Seq ID No. 188), MY120 (Seq ID No. 189), MYB174 (Seq ID No. 36), MYB175 (Seq ID No. 37), MYB176 (Seq ID No. 52), and sequences fully complementary thereto.
 7. A probe of claim 1, wherein said HPV type is HPV-42, and wherein said probe is selected from the group of probes consisting of MY33 (Seq ID No. 192), MY34 (Seq ID No. 193), MY121 (Seq ID No. 190), MY122 (Seq ID No. 191), WD169 (Seq ID No. 83), and sequences fully complementary thereto.
 8. A probe of claim 1, wherein said HPV type is HPV-45, and wherein said probe is selected from the group of probes consisting of MY68 (Seq ID No. 194), MY69 (Seq ID No. 195), MY70 (Seq ID No. 196), MY98 (Seq ID No. 197), MY99 (Seq ID No. 198), MY100 (Seq ID No. 199), MY108 (Seq ID No. 200), MY129 (Seq ID No. 201), WD171 (Seq ID No. 91 ), and sequences fully complementary thereto.
 9. A probe of claim 1, wherein said HPV type is HPV-51, and wherein said probe is selected from the group of probes consisting of MY87 (Seq ID No. 202), MY88 (Seq ID No. 203), and sequences fully complementary thereto.
 10. A probe of claim 1, wherein said HPV type is HPV-52, and wherein said probe is selected from the group of probes consisting of MY80 (Seq ID No. 204), MY81 (Seq ID No. 205), MY82 (Seq ID No. 206), and sequences fully complementary thereto.
 11. A probe of claim 1, wherein said HPV type is HPV-53, and wherein said probe is selected from the group of probes consisting of MY101 (Seq ID No. 207), MY102 (Seq ID No. 208), MY103 (Seq ID No. 209), MYB182 (Seq ID No. 38), MYB159 (Seq ID No. 39), and sequences fully complementary thereto.
 12. A probe of claim 1, wherein said HPV type is HPV-54, and wherein said probe is selected from the group of probes consisting of MY111 (Seq ID No. 210), MY112 (Seq ID No. 211), MY113 (Seq ID No. 212), MY114 (Seq ID No. 213), MYB160 (Seq ID No. 40), MYB161 (Seq ID No. 41), and sequences fully complementary thereto.
 13. A probe of claim 1, wherein said HPV type is HPV-55, and wherein said probe is selected from the group of probes consisting of MYB170 (Seq ID No. 42), MYB15 1 (Seq ID No. 43), MYB171 (Seq ID No. 44), MY151 (Seq ID No. 214), MY152 (Seq ID No. 215), MY153 (Seq ID No. 216), and sequences fully complementary thereto.
 14. A probe of claim 1, wherein said HPV type is HPV-56, and wherein said probe is selected from the group of probes consisting of MYB196 (Seq ID No. 45), MYB197 (Seq ID No. 46), MYB198 (Seq ID No. 47), MYB199 (Seq ID No. 48), and sequences fully complementary thereto.
 15. A probe of claim 1, wherein said HPV type is HPV-57, and wherein said probe is selected from the group of probes consisting of MY154 (Seq ID No. 217), MY155 (Seq ID No. 218), MY156 (Seq ID No. 219), and sequences fully complementary thereto.
 16. A probe of claim 1, wherein said HPV type is HPV-58, and wherein said probe is selected from the group of probes consisting of MY93 (Seq ID No. 220), MY94 (Seq ID No. 221), MY179 (Seq ID No. 59), and sequences fully complementary thereto.
 17. A probe of claim 1, wherein said HPV type is HPV-59, and wherein said probe is selected from the group of probes consisting of MY123 (Seq ID No. 222), MY124 (Seq ID No. 223), MYB172 (Seq ID No. 49), MYB173 (Seq ID No. 50), MYB162 (Seq ID No. 51), and sequences fully complementary thereto.
 18. A probe of claim 1, wherein said HPV type is HPV-68, and wherein said probe is selected from the group of probes consisting of MYB191 (Seq ID No. 66), MYB192 (Seq ID No. 53), MYB193 (Seq ID No. 54), MYB194 (Seq ID No. 67), MYB195 (Seq ID No. 55), and sequences fully complementary thereto.
 19. A purified sequence-specific oligonucleotide probe, wherein said probe consists of a nucleotide sequence which hybridizes under sequence-specific, stringent hybridization conditions to a nucleic acid sequence from a human papillomavirus (HPV), wherein said nucleic acid sequence is selected from the group consisting ofSEQ ID NO: 14 or the sequence fully complementary thereto, which is from HPV isolate 36A; SEQ ID NO: 15 or the sequence fully complementary thereto, which is from HPV isolate 36B; SEQ ID NO: 16 or the sequence fully complementary thereto, which is from HPV isolate 88; SEQ ID NO: 17 or the sequence fully complementary thereto, which is from HPV isolate 238A; SEQ ID NO: 18 or the sequence fully complementary thereto, which is from HPV isolate 238B; SEQ ID NO: 19 or the sequence fully complementary thereto, which is from HPV isolate 155A or 155B; SEQ ID NO: 20 or the sequence fully complementary thereto, which is from HPV isolate C14; SEQ ID NO: 273 or the sequence fully complementary thereto, which is from HPV isolate B6062; SEQ ID NO: 274 or the sequence fully complementary thereto, which is from HPV isolate D3173; SEQ ID NO: 275 or the sequence fully complementary thereto, which is from HPV isolate 7552; SEQ ID NO: 276 or the sequence fully complementary thereto, which is from HPV isolate JB10; SEQ ID NO: 277 or the sequence fully complementary thereto, which is from HPV isolate Lavc5; SEQ ID NO: 278 or the sequence fully complementary thereto, which is from HPV isolate D7515; SEQ ID NO: 279 or the sequence fully complementary thereto, which is from HPV isolate Pap116; SEQ ID NO: 280 or the sequence fully complementary thereto, which is from HPV isolate W13b; SEQ ID NO: 281 or the sequence fully complementary thereto, which is from HPV isolate Lavb24a; SEQ ID NO: 282 or the sequence fully complementary thereto, which is from HPV isolate Lavb24b or PAP291; SEQ ID NO: 283 or the sequence fully complementary thereto, which is from HPV isolate B8988; SEQ ID NO: 284 or the sequence fully complementary thereto, which is from HPV type 35; SEQ ID NO: 285 or the sequence fully complementary thereto, which is from HPV type 39; SEQ ID NO: 286 or the sequence fully complementary thereto, which is from HPV type 40; SEQ ID NO: 287 or the sequence fully complementary thereto, which is from HPV type 42; SEQ ID NO: 288 or the sequence fully complementary thereto, which is from HPV type 45; SEQ ID NO: 289 or the sequence fully complementary thereto, which is from HPV type 51; SEQ ID NO: 290 or the sequence fully complementary thereto, which is from HPV type 52; SEQ ID NO: 291 or the sequence fully complementary thereto, which is from HPV type 53; SEQ ID NO: 292 or the sequence fully complementary thereto, which is from HPV type 54; SEQ ID NO: 293 or the sequence fully complementary thereto, which is from HPV type 55; SEQ ID NO: 294 or the sequence fully complementary thereto, which is from HPV type 56; SEQ ID NO: 295 or the sequence fully complementary thereto, which is from HPV type 57; and SEQ ID NO: 296 or the sequence fully complementary thereto, which is from HPV type 59; andwherein said probe does not hybridize to a genomic sequence from HPV types 6, 11, 16, 18, and 33 under said conditions.
 20. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 14 or the sequence fully complementary thereto, which is from HPV isolate 36A.
 21. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 15 or the sequence fully complementary thereto, which is from HPV isolate 36B.
 22. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO; 16 or the sequence fully complementary thereto, which is from HPV isolate
 88. 23. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 17 or the sequence fully complementary thereto, which is from HPV isolate 238A.
 24. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 18 or the sequence fully complementary thereto, which is from HPV isolate 238B.
 25. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 19 or the sequence fully complementary thereto, which is from HPV isolate 155a or 155B.
 26. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 20 or the sequence fully complementary thereto, which is from HPV isolate C14.
 27. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 273 or the sequence fully complementary thereto, which is from HPV isolate B6062.
 28. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 274 or the sequence fully complementary thereto, which is from HPV isolate D3173.
 29. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 281 or the sequence fully complementary thereto, which is from HPV isolate Lavb24a.
 30. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 283 or the sequence fully complementary thereto, which is from HPV isolate B8988.
 31. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 279 or the sequence fully complementary thereto, which is from HPV isolate Pap116.
 32. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 275 or the sequence fully complementary thereto, which is from HPV isolate
 7552. 33. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 277 or the sequence fully complementary thereto, which is from HPV isolate Lavc5.
 34. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 282 or the sequence fully complementary thereto, which is from HPV isolate Lavb24b or PAP291.
 35. A probe of claim 19, wherein stud nucleic acid sequence is SEQ ID NO: 280 or the sequence fully complementary thereto, which is from HPV isolate W13b.
 36. A probe of claim 19, wherein said nucleic acid sequence is SEQ. ID NO: 278 or the sequence fully complementary thereto, which is from HPV isolate D7515.
 37. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 276 or the sequence fully complementary thereto, which is from HPV isolate JB10.
 38. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 284 or the sequence fully complementary thereto, which is from HPV type
 35. 39. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 285 or the sequence fully complementary thereto, which is from HPV type
 39. 40. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 286 or the sequence fully complementary thereto, which is from HPV type
 40. 41. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 287 or the sequence fully complementary thereto, which is from HPV type
 42. 42. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 288 or the sequence fully complementary thereto, which is from HPV type
 45. 43. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 289 or the sequence fully complementary thereto, which is from HPV type
 51. 44. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 290 or the sequence fully complementary thereto, which is from HPV type
 52. 45. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 291 or the sequence fully complementary thereto, which is from HPV type
 53. 46. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 292 or the sequence fully complementary thereto, which is from HPV type
 54. 47. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 293 or the sequence fully complementary thereto, which is from HPV type
 55. 48. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 294 or the sequence fully complementary thereto, which is from HPV type
 56. 49. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 295 or the sequence fully complementary thereto, which is from HPV type
 57. 50. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO: 296 or the sequence fully complementary thereto, which is from HPV type
 59. 51. A primer for amplifying HPV-51 nucleic acid, wherein said primer is selected from the group of primers consisting of CEG05 (Seq ID No. 94), HMB01 (Seq ID No. 95), HMB02 (Seq ID No. 96), HMB03 (Seq ID No. 97), and HMB04 (Seq ID No. 98). 